As pointed out in the documentation;
Recover edited files
When a user edits a file, that file is also downloaded and saved to the Atlassian Companion folder on their computer. Files are cleared every time the Companion app restarts.
Follow our guide to accessing Confluence files edited with the Atlassian Companion app.
it would explain why files become missing. Is there any way to disable this feature? All of our users are reporting back that data is getting lost because files are no long available. Trying to "recover" files, only leads to empty directories.
Thanks,
Phil