Hi Joe,

You only need to disconnect the battery completely if you are using a "negative pulse" (sometime called "reflex") charge mode. This mode applies a very brief (usually around a millisecond) negative pulse to the battery. This is what will damage the ECU.

You should find out if this Astroflight charger uses negative pulse charging as neither Bob or myself are familiar with it.

Let me know if I can help any further,

Regards,