Yup. Everybody knows that’s dumb. That was the first thing that had got me looking at MTP. If you remember it was the first thing I was asking about mouse click macroes, and so I ended up with MIDI Buddy. The original Launch Control was the controller I first set up with mute/solo button mouse clicks. Have used the same translators you had sent me ever since. Just copy/paste them, set the mouse click position and set the in/outs.
But in the meantime after replying here, I had figured it out. The factory template is the offender.
I have the controller disabled in the FLS MIDI settings. So I run everything it does through BMTP#3 virtual port (set as 27 in FLS). If you remember, I had a struggle with whether to have the knobs and buttons seperate, or just have everything run through MTP.
So I didn’t care to bother with whatever driver it was set to in FLS. But apparently it matters.
Even though it’s disabled, If I set it to “generic controller” the old links disappear. Setting it back to factory makes them appear again, and they can’t be deleted as normal. So the device is storing them onboard and Image Line’s ‘controller support’ I mentioned earlier is causing this. Actually your mention of it made me read that page again and see the words, “auto detect”. Leading me to find the culprit.
So I just have to set it to “generic controller” (even though it’s disabled and doesn’t communicate with FLS at all), and the problem is solved, but it reverts back to the one I don’t want on every boot up (factory), so unfortunately I have to redo this setup every time. I just finished telling IL about it.
Also have been working on my MTP project, to reset all the links (because of this problem). So I have all fresh MTP presets and new links set up. All new mouse click macroes on the buttons. Everything done except the button lights; don’t even know if I will bother with that.
56 parameters X 6 user banks. 336 links, new inputs set, new outputs set, renamed, relinked in FLS. New positions for mouse clicks on my new FLS template. Been doing this for two days, and some other keyboard things. Don’t want to change it now.
I never use the factory mode and never will. I can’t stand it, or having these companies tell me how to use these things, when I prefer to customize it in MTP how I like. So that means you’ve been working hard helping me and I’ve been rejecting everything you’ve been doing. Sorry, feel bad about that. 
MCU is good in FLS for transport controls. I use MCU for my NI S61 MKII. Have to redo that controller too. I’m going to make better data back ups from now on. My MTP project survived, but it’s a version from like a year ago.
Funny you mention MCU. I just got a Mackie mixer and of course it has some really bad design things on it too. I just can’t win.