Layering on Peter Gulia’s excellent summary, it is difficult to determine when the relationships among the participating employers not are related (or whatever) enough to qualify for the exemption from registration. However, in one arrangement in my experience, the decision was to disassemble and have some of the employers go their separate ways with their-spun off plans. I am not aware of any enforcement action or participant claim of violation.
The real problem is you amended one of the key data points that their computers use to track 5500s. To the computer the amended return look like an amendment to a return that didn't exist. You should be able to get it fixed once you get the situation in front of a human. It won't be easy because since Covid working with the IRS has been hard. However, with persistence this will most likely end with no penalty.
If you were amending anything OTHER than the EIN or Plan number, it probably wouldn’t be an issue.
But those things can cause issues because if you filed a return without the proper identification, did you really file timely? It’s going to take additional correspondence and work to fix but should be resolved. Just not quickly.