You'll have to synchronize multiple system tables
If you just load 1 user database and don't want to change syslogins in master database, then you have to check several tables in the user db, including: sysusers, sysroles, sysreferences
If you use column encryption and if you store your encryption keys in different db, then you also have to check syscolumns
If you load all user databases, it's easier to sync your master database, check tables:
- syslogins
- syssrvroles
- sysloginroles
- sysattributes (for remote logins, nested roles, some login options, etc.)
- sysroles
- sysusers
- sysprotects
Note: directly updating system tables is not supported...