I made a part based in a Ard Mega, and now when I click on some pins in SCH other pins light up yellow like they are connected.
How do you disconnect internal links?
Have you checked in the editor? Under the list of pins on the right there is a check box that says set internal connections. Once checked it will show any internal connections as ratsnests. You can then right click on those and delete them.
I remember seeing it just couldn't remember where, either that or 6hr of part making got to me,
Never used it before, quite interesting how it works.