After class changing MP of spells from previous class goes down/up to 3 (it looks like this: 3/3/3/3/3/3/3), so it's good idea to class change instantly after getting highest level spells, because you get 2 MP for free without further leveling in this class.
Apparently the Alchemist => Hunter class change is expection for some reason and you save all your MP.

That's because, for whatever reason, one of the Hunter's skills is internally treated as a spellcasting skill, but the corresponding csv file gives that skill zero casts per spell level at all levels. It is possible to mod the game so that the skill gives Hunters alchemy spellcasting.

If you change from a spellcasting class to another that gets the same type of magic, your MP for the class doesn't change. If you change to a class that does not share that type of magic, you get 1 MP per spell known to a maximum of 3 per level (even if there are 4 spells of that type and level).

If you are missing spells for your previous class, you can learn them if you know at least one spell of the level, provided that:
* If your new class can learn that type of magic, you are high enough in level to learn the missing spell.
* If your new class can't learn that type of magic, you are high enough that a pure caster at your level would be a high enough level.

This does mean that going Cleric 13->Lord will cause you to take longer to learn missing spells than if you went Cleric 13->Fighter. (Not all of the game mechanics make complete sense.)

Edit: I haven't tested it, but I suspect Alchemist->Hunter, as a special case, *will not* learn any missing Alchemist spells, which means you will not want to use Protectorate with that character. (Being level drained or casting Miracle could also make you go down to 3 MP per level, I suspect, for this case.)