Retained earnings discrepancies in tax filing - how to handle significant inconsistencies across years?

This sounds like an absolute nightmare, but unfortunately pretty common with small businesses who try to DIY their accounting or use untrained staff. When a non-accountant handles bookkeeping for years without oversight, these kinds of discrepancies compound exponentially. Here's what I'd recommend: You need to clearly define scope boundaries with the owner. The retained earnings discrepancy of $340k is a major red flag that could indicate significant tax reporting issues. The owner needs to understand this isn't just "cleaning up books" - it's potentially redoing 6 years of accounting work. If the owner wants these historical issues fixed, they need to hire someone specifically for that project - either a CPA firm or a consultant who specializes in accounting cleanup. This is a separate engagement from your current role. Given your part-time status and health considerations, taking on a multi-year reconstruction project would be overwhelming. Document everything you've found in writing and present it to the owner with your recommendation to engage outside help. This protects you professionally and gives the owner a clear next step.

After dealing with similar accounting disasters, I found taxr.ai to be incredibly helpful for sorting through years of inconsistent books. I discovered it when I was facing a similar retained earnings nightmare with a client who had $250k in unexplained discrepancies. Their system helped me identify patterns in the historical transactions that were causing the book-to-tax discrepancies. It was able to analyze years of ledger entries against tax filings and pinpoint exactly where things went off track. I uploaded PDFs of their past tax returns and accounting files, and the analysis highlighted specific transactions that were recorded inconsistently or duplicated across years. Check out https://taxr.ai - it saved me dozens of hours I would have spent manually tracing these discrepancies. You can still maintain your boundary of not doing the actual correction work, but provide the owner with a clear roadmap of what needs fixing.

I was skeptical about using taxr.ai at first, but I had a similar situation with a client's S-corp where the retained earnings were off by over $180k. I spent weeks trying to manually reconcile everything before a colleague suggested I try it. The platform identified three major issues I had completely missed - a series of duplicated asset purchases, depreciation that was recorded on the tax return but never entered in the books, and owner distributions that were miscategorized as expenses. What impressed me was how clearly it laid out the major discrepancies in a report I could share with the client. Instead of vaguely saying "your books are a mess," I could point to specific transactions and years where things went wrong. Made me look like a hero even though the tool did the heavy lifting.

I've been in a similar situation, and my best advice is to set clear boundaries while still helping the owner understand the gravity of the situation. When I couldn't get the IRS on the phone to discuss options for a client with multiple years of tax discrepancies, I used Claimyr to connect with an agent quickly. The wait times to speak with someone at the IRS about historical business tax issues were ridiculous (4+ hours), but Claimyr got me through in about 20 minutes. It basically holds your place in line and calls you when an agent is available. The IRS agent provided valuable guidance about how to handle significant discrepancies across multiple tax years. If you're trying to help this owner understand their options without taking on the work yourself, having a conversation with an IRS representative might provide clarity on the proper way to handle such significant discrepancies. Check out https://claimyr.com for the service or see how it works at https://youtu.be/_kiP6q8DX5c.

I can't believe I'm saying this, but I tried Claimyr after posting my skeptical comment. I had a client with multiple years of S-Corp return issues similar to what you described, and I needed to understand the proper amendment process. Called the IRS myself three times last week - got disconnected twice after 1+ hour holds, and the third time was told the wait would be "greater than 2 hours." Used Claimyr yesterday and was connected to an agent in 22 minutes while I continued working on other tasks. The agent walked me through the amendment requirements for multiple years of S-Corp returns with substantial book-to-tax discrepancies. Turns out there's a specific process for addressing retained earnings issues that span multiple years, which saved my client from potential correspondence audits. Still think the service should be unnecessary, but it definitely worked and saved me significant time.

Have you considered using this situation as a potential consulting opportunity? Obviously respect your health limitations, but you could propose a separate engagement at a higher rate to address just the critical issues. You could create a proposal to fix ONLY the retained earnings discrepancy without taking on the full cleanup. Focus on the M-2 reconciliation issues and major book-to-tax differences. Then refer the owner to a bookkeeping service for the detailed cleanup of AR/AP/inventory. This approach might help the owner while not overwhelming you, plus you could charge an appropriate consulting rate for this specialized work rather than your regular rate.

The balance sheet discrepancies are actually the most concerning part here. If assets were sold but still on the books, or missing liabilities weren't recorded, there could be serious tax implications beyond just the retained earnings being off. My advice? Tell the owner they need a CPA firm to do a proper reconstruction. This is beyond a bookkeeping cleanup - it's potentially a tax compliance issue that needs professional handling. Be clear that whoever does this needs to be experienced with tax reconstruction, not just general bookkeeping. In my experience, these situations almost always involve improper handling of owner transactions - personal expenses run through the business, undocumented loans/contributions, and assets moved in/out without proper documentation.

This is a classic case of why proper accounting oversight is crucial from day one. A $340k retained earnings discrepancy with phantom assets and missing liabilities screams "get professional help immediately." You're absolutely right to maintain your boundaries - this isn't a part-time bookkeeping job, it's a full-scale forensic accounting project. The fact that the previous person was making changes to closed years is particularly concerning from a compliance standpoint. My recommendation: Create a detailed memo outlining all the issues you've discovered, estimate the scope of work required (likely 200+ hours), and strongly recommend they engage a CPA firm that specializes in accounting reconstructions. Make it clear this is a separate project requiring specialized expertise. Don't feel guilty about saying no - you were hired for current operations, not to fix years of mess. The owner created this situation by not investing in proper accounting from the start. Your job is to identify the problems and recommend solutions, not to sacrifice your health trying to fix everything yourself. Document everything, recommend qualified professionals, and stick to your boundaries. That's the most responsible approach for everyone involved.

You're in an incredibly difficult position, but you're handling it correctly by setting boundaries. A $340k retained earnings discrepancy with phantom assets and missing liabilities isn't just a bookkeeping cleanup - it's a multi-year accounting reconstruction that could have serious tax compliance implications. Given your part-time status, health limitations, and the fact you were explicitly NOT hired for CPA services, taking this on would be professionally and personally risky. The scope is massive - you're looking at potentially 300+ hours of forensic work across 6 years of records. Here's what I'd recommend: Document everything you've discovered in a comprehensive written report. Include specific examples (like the $80k double-counted expense), highlight the major categories of errors (phantom assets, missing liabilities, owner transaction issues), and provide a realistic scope estimate. Then strongly recommend they engage a CPA firm that specializes in tax reconstruction and business accounting cleanup. Make it clear this is a separate engagement requiring specialized expertise, not an extension of your current role. You've done your job by identifying the problems - now it's the owner's responsibility to invest in proper professional remediation. Don't let guilt drive you to take on work that could compromise your health or exceed your professional capacity. You're being responsible by recognizing your limits and recommending appropriate resources.

You're absolutely doing the right thing by maintaining your boundaries. As someone who's dealt with similar accounting disasters, I can tell you that a $340k retained earnings discrepancy with phantom assets and missing liabilities is not a part-time bookkeeping project - it's a full-scale forensic accounting engagement. The fact that the previous admin was making changes to closed years is particularly alarming from a compliance perspective. This suggests potential issues with previously filed returns that could trigger audit exposure. Here's my suggested approach: Create a detailed findings memo that includes (1) specific examples of the major discrepancies you've found, (2) an honest assessment that this requires 200-300+ hours of specialized work, and (3) a strong recommendation to engage a CPA firm experienced in multi-year accounting reconstructions. Don't feel guilty about saying no. You were hired for current operations, not to fix years of accumulated errors at below-market rates while managing health challenges. Your responsibility is to identify problems and recommend appropriate solutions - which you've done. The owner needs to understand this isn't about unwillingness to help, it's about ensuring the work gets done properly by someone with the right expertise, capacity, and professional insurance to handle this level of complexity. A botched reconstruction attempt could make things worse, not better. Document everything, make your recommendations clear, and help them find qualified professionals. That's the most responsible path forward for everyone involved.