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Mex5150 - maybe you could run a 'watch for deletes' monitor on the library tree, see ==>>
Monitor file system activity with inotify - probably filter by the format types (PDF, EPUB, MOBI etc), log or pop a message when delete happens
BTW I'm with you on the library folders - I dive in and out of them all the time. But I never add new items (folders or files), or delete or rename existing items. And I've never lost anything, or had Check Library report significant errors.
BR