After you've used Extra|Compare Files or Extra|Compare with File on Disk, the files you compared may have their differences highlighted. If you're done comparing the files but want to continue working with them in EditPad Pro, select Clear Comparison Marks in the Extra menu to remove the red and green highlights.
If you don't want to continue working with the files, simply close them. You don't need to remove the comparison marks first.
Extra|Compare with File on Disk