https://wiki.mikrotik.com/wiki/Manual:C ... escription
The configuration backup can be used for backing up MikroTik RouterOS configuration to a binary file, which can be stored on the router or downloaded from it using FTP for future use. The configuration restore can be used for restoring the router's configuration, exactly as it was at the backup creation moment, from a backup file. The restoration procedure assumes the cofiguration is restored on the same router, where the backup file was originally created, so it will create partially broken configuration if the hardware has been changed.
Yes, this is expected behavior. Use config export/import instead.