Before an output file is created, every time a source file is added or removed, the output file name is recalculated. After an output file is created, adding or removing a source file does NOT recalculate the file name. I often create an mkv file, then afterwards I want to create a subtitle mks file. At present I have to close MKVToolNix and reopen it by dragging the newly created mkv file to it, de-select all source files but the subtitle, then clicking “Start multiplexing” to create an mks file. It would be easier for me if adding or removing a source file(s) after creating an output file caused to file name+extension to be recalculated.
Welcome!
Removing all source files from a multiplex job is not the same thing as using a completely new, pristine multiplex job. This is on purpose. If you want to start over fresh, open a new multiplex job for it (“Multiplexer” menu → “New”).
You most likely fail to realize that the GUI uses an approach similar to browser tabs. You can have as many multiplex jobs (browser tabs) open simultaneously as you want. No need to restart it all the time.