Hello.
I'm really sorry to hear this.

The extension cannot delete the stored bookmarks, it's impossible because there isn't a command that does that, so I'm 100% sure it's not possible.
Something like this can happen only if you uninstall the extension when the bookmarks are locked or if something wrong happens to Firefox and the extension's database is somehow cleared. Maybe an update or something. Of course this is not under my control and there is no way to recover them if this happens.

The only solution is to backup your Firefox profile every once in a while, it contains also the extensions and their databases, which means that if the database is cleared for some reason, you can load the old backup and you should find all the bookmarks (if they were locked, you'll find them still locked and I recommend that you leave them locked so that they won't be accessible in the backup). I've just tried this and it worked.

You can see the location of the profile by writing this in the address bar: about:profiles
Once you are there, you'll see the profile that is being used and you can backup the content of both the root and the local directory (B).
If this happens again, and I hope it doesn't, you can replace the content of the current profile (A) with the content of the old backup (B). Of course don't delete the current profile (A) but save it somewhere. After the change you'll be able to unlock the old bookmarks and export them. Once you have exported all the bookmarks, you can reload the current profile (A) by replacing the backup (B), import the bookmarks and lock them.
I know this is a little annoying but it's the only way to make sure you don't lose all the bookmarks.

Again, I'm sorry for what happened but I can tell you for certain it wasn't caused by the extension itself.
I hope that you can recover as many bookmarks as you can and by following the instructions above you should be able to prevent this.