Sync isn't to be used as a backup it only sync data from the accounts connect to the devices logged into the Firefox account. And sync doesn't update instantaneous as one thinks it takes sometime for sync to update faster then others. So is the other computer Linux on and connected to the internet so the Windows computer version can get the correct data sync. You need to insure this in-case connections is lost or sync doesn't complete. Beyond that unless you followed Firefox FAQ on how to backup the data there nothing much that can be done here.