I can't comment on your Unix/Linux environment. We are solely a Windows shop (Baan was the only Unix application we had until we migrated to Windows many years ago)...
However, the only files that needed to be changed were in the $BSE\lib\msql\ directory. They were: msql_users and msql_groups
These were the only files that we needed to change when creating the test environment. I thought that there might be others for the Baan application but there were not. We did disable all of the automated batch jobs on the new server so that they would not continue to run (some of them send notification e-mails out to users).
The only real issue we ever came across was that since out 3rd Party DBA was not Baan savvy, the group permissions on the new database would not be set up correctly because they would have to correspond with the new database name. Once those were re-established we were fine. We use a NazDaq-IT product to change the color of our environment so users would know they were in the test environment vs production.
Hope this helps.