Look into your Backup plugin which is exporting a JEX backup every night for each profile. Locate the path in the backup plugin settings. Can you find both JEX backups for both profiles?
To start over from a JEX backup: How to fix synchronisation issues and start over
You can have two profiles each synced to their own sync target. Just don't sync them to the same ms account. If you really want to use ms for both, sync to two different ms accounts.