IDE is not very good working with same instances of the code. Indexer, Problem markers, Debugger breakpoints would be 
mess all the time.
I suggest close same code-base projects which are not required immediately and only have one instance of branch in 
workspace (which is open).

Personally I use same project in workspace for all variances, when I need to apply something on branch I use same 
project with "Switch to Another Branch" command from Team set
(which works correctly for CVS and SVN), then apply patch and switch back. To move changes between project I create 
Patches using Team->Create Patch...
Same works for multiple projects (I can select and switch several project at the same time). You just have to be aware 
that when you switch you loose your local changes,
so everything has to be committed before or stored in patch.

Mario Charest wrote:
> This is a situation reported to me by co-worker.
> 
> Windows Host IDE 4.5 setup for 6.3.2 and custom makefile.  Most people work on multiple project at the same time which
 are all branches (SVN) of the same root project .  When building a project, the Problems view will show the error but 
will specify the resource as being from another project then the one from which the make target was launch.
> 
> I'm also told that when "Opening Declaration" of a symbol a windows with multiple choice shows up that offer items 
that are in other projects. 
> 
> Is there any way to disassociates projects.
> 
> 
> 
> _______________________________________________
> General
> http://community.qnx.com/sf/go/post20492
>