That sucks. Do you know of any way to fix it, other than backing up the data in each app separately using means other than iTunes/iCloud backup, and then restoring the iPad to factory state, which would take hours?
What did you use to sync? I've been able to sync Git repositories in GoodReader and Working Copy, but I have found the Files app's SMB support, and integration with apps like Secure Shellfish, to be buggy and unreliable.
The device needs a factory reset. Deleting the Files app itself does nothing, even though this warns you that all associated data will be deleted. Which is unsurprising at this point. The latest OS updates feel like I'm a beta tester for Windows ME.
What did you use to sync? I've been able to sync Git repositories in GoodReader and Working Copy, but I have found the Files app's SMB support, and integration with apps like Secure Shellfish, to be buggy and unreliable.