The plugin does not support different line endings, like "\n" and "\r\n", in the files to compare.
While comparing it sometimes inserts new lines into the files. When clearing the results (to get rid of the additional lines) it destroys the end of some lines! This happens when the line originally ended with a single "\n" character which will be replaced with "\r\n", overwriting the end characters of the line (does not matter if whitespace or not).
This behaviour, together with the "feature" of deleting the Undo-Queue is CRITICAL! Unsaved files can't be restored and (depending of the number of compares and resets) quite big parts of some lines in the file are lost before the user recognizes this.
(I'm using Notepadd++ v6.1.8 (UNICODE) with Compare v184.108.40.206.)