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)