When you are using the Filesystem as the backend for saving your documents, the content of your documents is stored in the upload folder, so you should backup that folder too. Also, when you change the backend you can't access all files you saved with the other backend. We'll have to do something about it, but currently that's how it woks

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In order to delete those broken files you would have to manually delete them from the database. This following queries would delete all files from OpenGoo.
DELETE from `og_project_files`;
DELETE from `og_project_file_revisions`;
If there are files that do work and you don't want to delete you would have to add a WHERE condition specifying only the files you want to delete:
DELETE from `og_project_files` WHERE `id` IN (1, 2, 4, 6);
DELETE from `og_project_file_revisions` WHERE ``file_id` IN (1, 2, 4, 6);
You can get the file ids with this query:
SELECT `filename`, `id` FROM `og_project_files`