If you enable multi charge and charge up till that amount, you can revert the multi chamber and still have that amount of charges to work with.
It does get set to the correct amount after using the module, but you already used it once by then so you always get 1 extra charge.

That's however a minor issue, you could for example swap out chambers quite fast and get benefits you then revert later on. Power efficiency 3 to charge fast, then reverting it out for Jump distance 3 to jump far. Takes only a few seconds.
Seems to me that the safest choice, is to always discharge every module completely, including weapons, after changing your reactor setup or switching reactors.

This should not discharge from combat damage though, or at least not like this.