ProGet most definitely does not "lose package" on an upgrade, so there must have been some sort of configuration change, either in the ProGet software (retention policy, package store), or external to the software (files deleted from disk).
It's highly unlikely that this configuration changed as part of the upgrade, particularly from those versions. Most likely, your database backups just happened to be dated from before the upgrade because the installer will auto-backup for you; so, the upgrade is really a red herring. You can search ProGet's audit logs to see if anyone in the software deleted them.
But regardless, if the package files are gone, and you don't have them backed up (the installer will not do this for you), then they are gone. There's nothing you can do, so I think your idea of searching for fragments from user caches, and then uploading those, is the best you can do.
NOTE: Unless you explicitly configured a retention policy for ProGet to delete files, the software will not delete these files on disk. Even when you delete a feed or uninstall the software, the package files remain. We do this for safety purposes.
Please make sure to read our backup and restore instructions.