The BLM's get cleared when disconnecting the orange wire. If you're using two radically different chips, the car will run poorly until warmed up (above 160 degrees) and the BLM's re-adjust. Many chip suppliers use the BLM's for other uses (to store parameters); so if you switched chips "hot" you may end up with unpredictable results.
However in the old days, if you're changing from a closed loop to an open loop chip (like the old Thrasher), it was actually better not to disconnect the orange wire.