the only thing I could think of would be to round up files by date - after an itunes backup and after whatever data loss occurred , save them to an external spot, then to restore from itunes backup. only thing is, I don’t know how one could thoroughly locate all files created or modified after a specified date.
An iCloud or iTunes backup restores everything saved to it. You can’t choose which file to restore, and you can’t save single files within the backup.