Just as you have a forced manual matching ability, there should be a forced manual mismatching.
I have the following:
old file matchs new 1 old file matchs new 1
XXXXXXXXXXXXXXX new file unique line 1
XXXXXXXXXXXXXXX new file unique line 2
old file unique line 1 XXXXXXXXXXXXXXXX
old file matchs new 2 old file matchs new 2
Currently the only way to get the "old file unique line 1" to not be compared to the unique line in the new file is by modifying the thresholds.
As a work around, I added an empty line to the new file and forced a manual match between it and the old file's unique line. This is not idea because it modifies the new file, and it shows up as a difference and not a unique line.
Instead of doing that, I would suggest allowing the user to force a mismatch.