If your chip has different timing tables for 3rd and 4th you need to leave it hooked up.
riding around with it unhooked for a long time will let road grime and corrosion onto the contacts. When you want to use it at a later days you're have flaky connections that will drive you crazy.
Personally I don't think that's your problem. If the TCC is mechanically locked, your engine will die when you stop. From what I understand there's not fluid path to the TCC in first, so that's not possible to kill the engine if it's electrical.
I do know that If I leave my manual TCC lockup switch engaged I can tell when the car downshifts, as it's harsher than normal.