External Merge Tool discarded files

I needed to resolve a merge conflict. I right clicked and choose "Launch External Merge Tool" and some windows flickered up which I wasn't able to see what they said.

I then recalled I had reinstalled my system and not set up Kdiff as I had used to.

However, now the files that had merge conflict appear to have changed as a result of my first "Launch External Merge Tool". They still appear with a merge conflict warning, but the diff view in SourceTree and Kdiff3 says there are no changes.

So it appear that whatever was the default action of External Merge Tool picked the original files over the incoming merge. Now I cannot seem to revert that.

Any idea what that External Merge Tool did by default? What that flashing dialog window said?

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The most stable fix is going to be resetting your branch to the pre-merge commit and re-running the merge. If that is going to waste too much time, you could try doing the merge again to see if the same conflicts get reported.

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