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We employ a model where we have on integration and one common development stream per UCM project. Project A is the trunk. Project B is a branch of project A created on baseline BL1 of the integration stream of project A. The development stream of project A has been later rebased using using baseline BL2 in the integration stream. So BL2 is a newer baseline compared to BL1.

The question is would the fact the project's A development stream and project's B development stream now have different foundation baselines (with project's A dev stream having a newer foundation baseline) affect merging from project's B development stream to project's A development stream?

I understand that there would be a lot of non-tivial merges as the difference is quite big, but need to be sure there won't be any fundamental problems with CC in this situation.

Thanks!

+1  A: 

Yes it would: it would be a sideway merge

You can see one side-effect in the question ClearCase wants to merge unchanged files after deliver to alternate target.

In your case though, the effect should be minimal:
Merging from B to A should not generate more conflicts than usual for modified files, except if those files (modified in B) are no longer present in A (because rmnamed in BL2):
then a manual merge of the parent directory of those files would be needed.

VonC