It seems that your problem is that Compare splits the screen into two ‘views’ and does not remove them after ‘Compare’ is done. Select the unwanted tab on the right or just click in the editable area. Then go to View->Move/Clone current document->Move to other view. It should restore your original environment.
Alternately close all tabs in the unwanted ‘view’.
The dual ‘view’ mode is actually a Notepad++ feature and can be used for many general editing tasks.