Hello,
The conversion process works independently for each pane in BC3. If the file on the left (or right) is the working copy, then %s will point to a copy of that file that BC created to work with, and %n will point to the original file. I would suggest using %s unless you absolutely need the original path.
If you are opening a file that is not the version you expect, you may need to setup your version control software to call BC3 and have it open the two versions you want to compare.
http://www.scootersoftware.com/support.php?zz=kb_vcs
Does this help clear things up? Let us know if you have any questions.
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