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Use baseless merge to merge items that are not directly branched from each other. To perform a baseless merge, you must use the tf merge command. When you perform a baseless merge, Team Foundation does not have any information about the relationship of the files in the branches.
You need to go to the command line and use tf merge /force e.g. tf merge $/TeamProject/DevBranch $/TeamProject/Trunk /force This should do what you want.
If you need to merge a specific changeset you need to use the following statement:
tf merge /baseless /recursive /version:C95654~C95654 branch2 branch1
(It means ONLY changeset C95654).
The commandline you are using means every changeset before and with C95654.
I had to use tfs paths for the two branches. Steps were: add both branches to the desired workspace; get latest; open a Windows powershell in the target folder. Get tfs paths
>tf workspaces /format:detailed
>tf workfold
Then use $paths for the branches. Same changeset number between the tilde ment baseless merge for one changeset.
>tf merge /baseless /recursive /version:C999~C999 "$/MyRepo/Current" "$/MyRepo/Development"
More here -- http://blogs.msdn.com/b/bharry/archive/2011/08/31/merge-enhancements-in-tfs-11.aspx
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