Sorry, by 'now' I mean recently. I think an update has started this warning, but, after googling about it, compacting appears to be something that should be done: Hence the kick a long to actually do a backup, before attempting to compact.
It probably wasn't an update, but more likely one or more folder file(s) was 20%+ full of "marked for delete" messages and it was time to clean-house, so it was likely a coincidence.
I think (in Thunderbird), if you right-mouse-click each folder, you can compact them one at a time to compact the mailbox file(s). Do this for all folders... inbox/sent/trash/etc.... If you open a cmd prompt and "ls -la" the folder, you'll see before/after file size cleanup reductions after compacting.
"Compacting" is something that needs to be done every now and then if mail is stored in mbox format.
I think mbox is easier to recover than individual files (maildir).
2 mbox gotchas that you need to be aware of are... make sure you have enough space to create a compacted file, so if your current inbox is 2GB, you should have 2GB of free space to create a new/compact file (and then the old file is deleted).
gotcha #2 is watch-out that your mbox file does not get too large. If you receive lots of pictures and videos, your inbox can quickly climb up to 2GB+ in size. Some file systems cannot handle files larger than 2GB in size. Some programs cannot handle files 2GB+ in size. Thunderbird is (or was until recently) a program that has 2GB file-size limit, example:
https://bugzilla.mozilla.org/show_bug.cgi?id=215450