To remove the saved session information, navigate to the place where Merge is storing it’s configuration information on your system. That area is known as the
Data directory (it’s not actually a folder named
Data unless you’re using a portable installation though, in which case look in the install folder for a folder by that name).
The location of that varies depending on your OS, so check out the documentation page on packages to see what the location is for your OS.
Inside of the configuration area there’s a folder named
Local, and inside of that folder is a file named
Session.sublime_session that represents the saved session information. Moving that file away or renaming will make Merge start with a new blank session.
If that works, you might want to report an issue and provide the devs the session file that caused the problem in case that helps then narrow in on what went wrong.