Ok, in TFS we have a main trunk branch and another branch, let\'s call it secondary. We have created a new file in the trunk but when trying to merge
"Now, when I try to merge a file which was created in trunk after secondary was branched, secondary is no longer listed as a target branch."
For that, right click on the file in Source Control Explorer and choose Branch instead of Merge. That will then bring up a dialog to specify the target.
Generally, you are better off merging trunk and secondary rather than pieces of it (easier to keep the branch consistent over time).