This issue has been driving me crazy for awhile.
I've been doing some deep digging and it looks like Helix is causing the problem.
Looks like it's been an issue since 2021.
Has anyone else had the problem where you want to use SEO and then the backend doesn’t work after renaming httaccess?
https://forum.joomla.org/viewtopic.php?t=985622
Joomla says Helix is causing this.