When i run the .exe file to update version 1.12.4 to 1.13.0 I get an error message that says, “A running instance of Cryptomator is found, using files marked for update. Please close it to continue.” I have no idea what file this is referring to as all files and software applications are closed when I’m doing this. Anyone know how to resolve this issue? Thank you!!
Welcome to the Cryptomator Community 
Well, Cryptomator ist still runnning, otherwise this message is not displayed.
The following post gives you a method to detect, if Cryptomator is still running:
Also check your Windows system tray (normally the right bottom corner), if you can see the Cryptomator icon there.