Is it safe to amend your taxes as a U.S. resident when your I correctly filed as single instead of married but separate?

Hi everyone, I’m helping my uncle with a complicated tax/immigration situation in California.

My uncle has been a U.S. resident for 3 years. He has been legally married but 100% no-contact with his spouse for over 15 years (they separated right after the wedding, no shared assets/kids). Since 2020, he has been filing as "Single" on his taxes. He recently realized this was an error and should have been filing as "Married Filing Separately" (MFS), which he is finally fixing now that he’s filed for a formal divorce in 2026.

We are worried about the consequences of amending 2020-2025 taxes:

Immigration: Will amending from "Single" to "MFS" flag him for an investigation? He plans to apply for citizenship in 3 years. Does "fixing" a past error look better or worse to USCIS than leaving an incorrect status on his record?

Covered California: He received subsidies for 2024/2025 based on his "Single" status. MFS usually disqualifies you from these subsidies. Is there an "Abandoned Spouse" or "Victim of Abandonment" exception that allows him to keep his insurance credits even if he files MFS? Does anyone have any experience with this?

I would appreciate any input!

Should he just wait until the divorce finalizes and continue doing his taxes as single and just wait a longer period to file for citizenship?