if a 5500 is filed on time but with a missing scedule (CPA audit report), what are the ramifications? the cpa report will be filed eventually but it is currently not complete. would the DOL consider the 5500 in fact filed or is an incomplete 5500 mean a late 5500? Is there anything that can be done besides filing the CPA report to minimize the damage?

What DOL can do and what they will do are not necessarily the same. My personal experience is that they will write asking for the audit report, and will not assess penalties if the report is furnished within the requested timeframe. Note that this timeframe is SHORT. I think they have the authority, though, to treat the return as incomplete and to assess penalties on that basis.

And no, I don't think there is anything you can do for damage control short of filing the audit report.

I haven't looked at this recently, but I think you could file under the delinquent filer program and pay a relatively small penalty versus a potentially big penalty. I don't think I'd do this, but it is an option for minimizing the damage.

My experience is that they will first ask for the audit. If you don't provide it within a fairly short time frame, then the 5500 will be formally rejected. Once formally rejected you still have 45 days to "cure" before the penalty will be assessed. See DOL Reg 2560.502©-2(B)(3).