Looks like mafia always reported the .js file as being not modified, though I did edit it in between the first and second calls to the script.
There were a couple of bugs here. I couldn't see why your Browser asked for If-Modified-Since for a .js file since I didn't think we were sending Last-Modifed for such files. Alas, we were.
Also, the whole code for checking if a file in the relay folder was modified was bogus; it "assumed" that any such file was not modified if it had seen it before; after all, that "saves time", as the comment said.
Both issues should be fixed in 12689.
Unfortunately, you need to clear your browser cache - but not KoLmafia's image cache, so it will reload quickly.
So if we go years (= at least two) without anybody seeing anything like that, we can close the issue ?-)
I don't guarantee that corruption of the visible elements of LockableListModel is what is causing everybody's slowdown as KoLmafia keeps running. It was an issue for you, but let's see if people continue to see issues and report them on this thread.
I don't think we can close this thread until Darzil declares himself happy.