Correcting TPA Errors While Correcting Delinquent Deposits - VFCP and 5330s

So I recently received a request to assist with a VFCP application. I was provided the total of missed deferrals, payroll date, recovery date, distribution of lost earnings and 5330s.

The failures occurred one in 2022 and twice in 2023.

The 5330 for 2022 is very vague and doesn't include the correct dates, but the amount used to calculate the excise tax doesn't match the VFCP calculator with the actual recovery and final payment dates OR even if I used the recovery date as the final payment date.

The 5330 for 2023 only includes one item which I can only assume adds the 2022 number to the lost earnings for 2023 instead of breaking them up by transaction and compounding the total, but this total is still off from what the calculator shows.

The lost earnings summary for 2022 matches the 5330 for participant allocations, but so does the 2023. I mean that the entire amount of what I believe was the combined lost earnings was allocated to participants in 2023.

I'm trying to get in touch with the TPA to see who taught them to fill out 5330s and how they came to their calculations. Regardless, it seems like the sponsor overpaid lost earnings by a around $100.

I can't use their documentation and evidence because it won't match the calculator so it looks like I have to redo everything including the 5330's. DOL hasn't started an investigation yet but has sent a few "poke the body" notices.

Does anybody have any other suggestions? And if I'm right and they did overpay lost earnings, is that a prohibited transaction in itself that needs correcting? We're talking a few pennies for the majority of participants and most aren't employed there anymore.

Did the TPA use actual rate of return, rather than the DOL calculator? 
Unless the TPA was told that the plan would be submitting the correction to VFCP, the calculator should not be (though it often is) used.

I'm also wondering why the same person or company isn't doing the lost earnings + Form 5330 + VFCP if the plan wanted all three. It seems unusual or inefficient to have someone different prepare just the VFCP submission. 

Actual rate of return is all I can think of but that is a wide disparity in earnings between 40,000+ and 9,000 in late deposits and virtually the same recovery date. As far as why, they used the TPA for the 5330's then somehow DOL got wind and "encouraged" them to apply through the VFCP and they brought it to us. Either way I still need to correct the 5330's for compounding and get documentation from the TPA on how they came to their calculations.

Depending on the facts, one of several earnings methods could be used.  If permit participant direction of investments, if not, if have automatic deferrals, if most affected participants are NHCEs, etc... or if actual return less than DOL calculator then use the DOL calculator (as it is a floor).  Ultimately, if the client is submitting this under VFCP it can use the DOL calculator.  To me, the client (you) should do it right and submit the VFCP filing accordingly and also file an amended 5330 with explanation.  In the VFCP filing the client should describe what happen edin the prior "correction" (and, if you cannot determine what happened, disclose that you don't know what was used to determine earnings in that correction) and then describe your "correction of the correction".  If the client paid too much in earnings, it should just disclose that fact and tell the DOL that it is not going to seek the return of those amounts.  The DOL should not have an issue with giving the participants an extra $100 (unless the $100 went to the plan sponsor's owner or only HCEs or something like that.  I would also disclose that the demographics of the affected participant group wasn't just the plan sponsor or only HCEs or something like that).  The worst thing about filing the amended 5330 is that the excise tax difference will likely be nominal (a % of a % is pretty low) and it sounds like the client might actually be seeking a refund.  I would also describe what you are doing with the amended 5330 in the VFCP.