After a system copy (refresh), RFC destinations will be overwritten by those of the source system (typically the production system) and the passwords will be lost.
In general, this is not something you want. So before the refresh, you need to export the RFCs & passwords, and then import them after the database copy.
For the export/import, you can use R3load as described there: Easy export/import of a few database tables using R3trans
List of tables
For RFCs, you can use the following list of tables
For SECSTORE, make sure both the export and the import happen while SAP is down.
This list should be valid for Netweaver 7.0 to 7.4.