During an upgrade, the Flame Gate can't be re-armed by selecting it. It can be re-armed by selecting a not-currently-upgrading Flame Gate and tapping re-arm all. If you are simultaneously upgrading both your Flame Gates (or only have one), there is no way to re-arm them. Appropriate behaviour should be either: a. Not re-armable during an upgrade, even via another Flame Gate or b. Re-armable by selecting the currently upgrading Flame Gate. Nb: As long as it hasn't "run out of fuel", the Flame Gate does continue to function whilst being upgraded.