I have not seen the problem in emacs lisp modes. I thought I had it narrowed down to modes where Eglot was enabled, but I'm no longer confident in that.

(Indenting a single line at a time works, it appears only indent-region is affected.)

that error looks familiar , but i can't remember what I did if anything to fix it. I use https://github.com/radian-software/apheleia to indent on save anyways, maybe that's a workaround for your issue.

I actually packaged up clojure-mode into a script, where the 'shbang' line is emacs, and call it from apheleia on-save, i can send it if you want it, but cljfmt, zstyle, etc much better options.

you might also want to try clojure-ts-mode, since it's a completely different indent engine / implementation of 'indent-region'

(setq load-prefer-newer t) can help avoid stale byte code, long shot though.

For unrelated reasons I did try clojure-ts-mode earlier, but reverted as there were some things I couldn't get to work properly. (Sadly my git history does not have good notes on why. I shall try again soon.) I'm doubtful that it will help, however, as the issue is not specific to Clojure mode, but also affects YAML mode and others. (Though not yet seen it in Emacs Lisp mode.)

never a bad time to switch to yaml-ts-mode too 😝 but yah, it’s not a root cause solution :)

ISTR the issue I had was around automatically running eglot in these buffers?

Am willing to try the ts-modes, but haven't been able to apply yet. Need to schedule some time for that.

add/move the #’eglot-ensure hook from prog mode , etc not sure i understand the question

treesit-auto will automatically remap all modes, yaml, etc