use bookmarks?

 

 

You can:

 Ellié Computing Merge allows the use of bookmarks in both File and Folder Comparisons.

In Folder Comparisons, bookmarks are set for an item (in all sources). They are saved in both Status (.ecms files) and Templates (.ecmt files) so that you can find quickly the files and folders you have marked during a previous comparison or merge operation. These are particularly useful when generating reports from the command line.
The "Select Bookmaked Items" menu item allows you to bookmark items anywhere in the folder tree view, then select them easily and apply an action (copy, delete, solve...)

See also