Yes. You cant file an amended 2023 5500-SF since there is no original 2023 5500-SF. You can file a 5500-SF, but not amended one at this point. Btw, if you have never filed a 5500-SF for this plan, this filing must also indicate "first return".
Unlikely, but the IRS will send you love letters, and it may take a bit to get it fixed.
What will happen is:
- The IRS will say that the 2023 Form 5500-SF was late.
- You will need to respond with your explanation that you filed an EZ, then found out that the circumstances were different. I have never had an issue doing this.
- The IRS will probably contact the client again looking for a 2024 Form 5500-EZ since you filed a 2023 Form 5500-EZ. Respond with the explanation.
Side question, how many years of EZ's do you need to fix, assuming 2023 was not the first year for the plan?