This is the case when a merge always gives a tree conflict for a complete merge. The shortcut to avoid this conflict and merge the code is that after merging the full trunk with this branch ... ignoring the tree conflict, merge the individual folders.
For instance:
/trunk /FolderA /FolderB /FolderC /branhes /Branch1 /FolderA /FolderB /Renamed Folder (Previously Folder C)
- Merge
/trunk with /branches/Branch1 - Merge
/trunk/FolderC with /branches/Branch1/Renamed Folder
Hurrah!!
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