Plan in and out of MEP with 5500SF reporting issues

We took over a plan in 2023 that was coming out of a MEP.

I wasn't involved in the conversion but I'm not sure I would have known better than who handled it since I don't have experience with MEPs.

This plan was an individual plan that went to the MEP in 2022.

They then went back to an individual plan in 2023 with us.

When we wrote the new individual plan in 2023 we thought it was a restatement of the 1st plan and not a new plan - that the MEP was part of the continuation.

The first plan was plan #001 and our restated plan was #001.

The prior TPA never filed a 2022 5500SF for the original plan as they thought the MEP was taking care of 2022.

The client got correspondence from the IRS about the missing 2022 5500SF for #001.

Meanwhile, before that correspondence was received we had filed a 2023 and 2024 5500SF for the post MEP plan using #001.

We have since redone the post MEP plan document to be a new plan established in 2023 with plan number 003.

We filed a final short plan year 2022 5500SF for 001 using the DFVC program.

We now need to amend the 2023 and 2024 filings that were done under 001 to file under 003.

I think we just do that and expect correspondence since I believe the DOL/IRS system goes by EIN and plan number.  We will likely get correspondence that the amended 2023 and 2024 are late.  Do we just let this happen and then explain when the correspondence comes?

Is this all correct thinking or should it be done another way?