A backup would be the only true way to recover from this type of thing.
The default backup tool would recover most of this stuff if you had a backup. Backupmenu is also another option again this is little help if you have no backups.

You may be able to recover old backup files hidden in your device manually. rtcom-eventlogger would have an old db for example.
HAM and your notification of updates will hopefully fix itself if you run the updates with the standard repos enabled.

I would recommend using hamsterfiler over filebox. But you may recover filebox by removing all it's files manually then reinstalling.

Because the corruption is unknown normal recommendation is to flash to have a clean system going forward. It may cause all sorts of fun in the future.