There were two reported instances recently where this would happen.
One was where you highlighted a list of files, knowingly or not, then moved to another tab or area of the program, appeared to highlight another file and delete it, whereas in fact the original list was still highlighted, and all those files were deleted. You should create a view to look at deleted files that MC knows about, and see if it is aware it deleted the files or not. I'm not sure if the "Fix broken links" would place a record in the deleted files database or not though, but if this first problem happened, the files should be recorded there. I think the major cause of that problem was fixed in MC21.0.25. 1. Fixed: When switching tabs, the delete command would still route to the previous tab in some cases.
The other problem was when multiple files were selected, changing the filename tag to something like a blank, or an invalid filename, could result in all files being renamed the same thing, or delete. There was a big thread on that. I believe that was fixed in MC21.0.24. 3. Fixed: If in-place editing was used to change the filename field to an invalid value (like blank, or a name without a path), MC would not report an error and the data for that file could be lost.
So I guess the files may have been lost when you were running one of those versions, and hit one of those problems. Hopefully it won't happen again.