How far away from 6.0.3 is the current server version ?   The point is that client compatability is supported for 1 major version less than the server.  i.e. 6.0.x server will accept 5.0.x clients.  If you're going up a point release for same version, just do it; clients will be fine.

 Don and I have been discussing this off-line, and the short answer is, no, in general, you cannot "merge" one RTC repository with another RTC repository (even if one was created as a clone of the other one).   For the SCM data, what you can do is use distributed deliver to replicate the SCM data to another repository, and then once the two repositories are back to the same version, you can use distributed deliver to merge the SCM data back.   For the work item data, you can use a combination of import and work item replication (via something like the Tasktop RLIA adapter) to get a subset of the work item data transferred.