When undoing, Aba will warn you if some file was changed since the replacement. You may want to apply these changes to the old version of the file, or to discard them.
The right pane shows the changes in the file selected in the left pane. Aba uses the console file comparison tool specified in Options. You can press Merge changes to run a merge tool (also specified in Options).
So, you have three options:
The file is automatically unchecked when the window is open and you change the file (by running the merge tool or by manual editing). So, the changed file will not be overwritten with its backup.
You can press Select All to discard the changes in all modified files, and Clear All to left all the files as is.