If I understand you correctly you need migrate Sitebuilder to new updated server? If so, migration should be done manually, as there are no migration tools in Sitebuilder. It can be done manually by moving Sitebuilder database and sites into new server, but could also be done with backup/restore utils:
/SB_ROOT/utils/sbbackup
/SB_ROOT/utils/sbrestore
Please note, backup tools included into Sitebuilder only after 4.0.0 release.
I can suggest you to wait for new 4.1 release, update both servers to this new version and after that perform migration with special backup utils, as there were several issues in these utils, but in new version all these issues are corrected.