Apparently, Craftsman made two different openers back in the 1990's. They program very differently from each other. The problem is, they both have Yellow buttons and therefore, can't be ID'ed simply by button color.
I'll call one "type A". Type A can be programmed for only one code at a time. There is no way to directly erase that code. Instead, you need to program in a new code, and that will replace (erase) the old code.
I'll call the other "type B". Type B can be programmed for multiple codes. As you program in each new code, it adds it to its list of older codes. You can delete all the learned codes by pressing and holding the Yellow button for 6 seconds.
Now, enter the MyQ....
On a "type A", there appears to be some magic done by MyQ that allows it to learn the MyQ's code without it automatically replacing (deleting) the existing handheld remote's code. I have no idea how they do this. Maybe someone from MyQ tech support would post a clue here.
On a "type A", there does not appear to be any way to delete the code learned from the MyQ. You can program in a new handheld remote's code, but such doesn't change, delete, or otherwise disturb the MyQ code. I wish I was wrong, and put out the hope that MyQ tech support would post a way, and prove me wrong with a way to delete the MyQ code.
On a "type B", pressing and holding the Yellow button for 6 seconds, seems to only delete only the handheld remote codes. It doesn't delete the MyQ code. I have read, but can't confirm, that pressing the Yellow button for 6 seconds a second time, immediately after the first, might possibly delete the MyQ code.