It was a disaster. Literally the most important thing for any VCS tool is to never ever delete file I don't want deleted. No more Jujutsu for me.
Someday someone will invent a VCS tool that doesn't suck. Today is not that day.
The other issue you ran into with ignored files becoming tracked is a known limitation. I agree that it's really annoying. We have talked about it many times before but we didn't have a proper issue for tracking it, so I created one now: https://github.com/jj-vcs/jj/issues/5596
It is _exceedingly_ hard to lose files in jj, it's actually emotionally frustrating reading the line "most important thing [..] is to never ever delete file" because that's the whole shtick in jj with the oplog and whatnot - so something like nuking secrets completely from a jj repo is a bit of a chore.
Can you file a bug at least? A repro of some sort?. Or at least show us what is it what you did, `jj op log` might be enough to deduce what happened.
Also check out `jj op log -p`, your files might very well be in history, especially if, as you said, jj status took a long time (presumably snapshotting those files that got lost)
