We rebuild our CPD files quite often, for precisely the kinds of synchronization issues you describe. The only problem we run into when we do so is that it can take a long time to rebuild for the really huge projects. For most people, this shouldn't be a problem.
Rick, your article still applies to RH6/RSC3 projects. FYI, I also remove the pss file and the mssccprj.scc (if present).
I haven't checked the procedure for RH7/RH8 projects, but I'll bet it's the same.
Leon, you might want to be careful with renaming items in source control. If you make a change in source control, RH may not know about it. We generally make changes in RH, letting RH communicate the relevant changes to RSC. I don't usually make changes directly in RSC unless there's a problem.
I might mention that such problems tend to occur when there is a RH crash during certain kinds of operations. For example, say that the help author renaming a folder when his or her pc crashes. This kind of interruption can leave RH with one set of information and RSC with another. Then you can get stuck with having to manually rename and delete things to get them sync'd up again.
I'll agree with you on deleting/hiding folders in RSC. Sometimes there gets to be quite a bit of visual clutter, but you probably don't want to totalll obliterate the old items.
So, I tried it out on one of my test systems.
Removing the project from source control will change that user's view of the project.
However, the user can re-connect to the project again (by opening it from source control) which will copy all the files back down as if it was new again.
However, if the issue you are having is that your authors are seeing different versions of the files, you should check on the status of the files for each user.
I reccomend you have each user save and check in all files.
This should put all changes back up. Then, when you open the project, have each user download the latest from the server. If there are any inconsistencies, you will get warnings about them.
Hope this helps.
Oh, One more comment.
You can disconnect a project from source control instead. This makes the local set of files on your PC a local only project, but leaves the stuff on the RSC for other authors to connect to.