I'm often using the excellent Kdiff3 tool to check/sync/merge folders with files of all kinds.
[PROBLEM]
Recently, I wanted to merge 2 folders but the "simlate" listing was empty...
Also, when I performed the actual merge operation, affected files/folders were marked "Done" but nothing had changed.
[SOLUTION]
Merge is applied to to folder "B".
So make sure that you A (Base) and B folders are chosen correctly.
If they are the other way around, you can simply swap them:
[*]File > Open
[*]Push button: "Swap/Copy Names..."
[*]Select: "Swap A<->B"
Then rescan (if not done automatically), and re-assign the desired merge operations.
Now it should work