Indexing Obsidian folder creates empty files, can you help fix?

That’s definitely not a DEVONthink issue; it’s a personnel problem
It is best to have tight controls over such a resource. If you are indexing such a group, people should not be allowed to remove files from it (or potentially add or rename either). If this is your folder on Google Drive, I would administer it much more carefully to avoid missing files in your database.