[edited from support email]

I believe there's currently no way to delete a file from a list you've created in Merge Files. If that is so, it would be great if you could add it to future updates. Otherwise, I'd love to know how it's done.

You can open the list and edit it in a text editor like Notepad, no?
Yeah, you're right... I tried it and it definitely works. However, you have to save the file, open it in notepad, then load it again in filemerge. It would definitely be easier if there was some possibility of manipulating the file list within FileMerge.