Hello.
The Master Chemist PrC describes
[ The mutagenic form shares memories and basic goals with the chymist’s normal personality but goes about meeting those goals in a different manner]
Does this mean the alchemist also remembers what their alter ego was doing?
Or merely that the alter ego remembers what the alchemist knows, and the alchemist has a blackout of events when the alter ego is behind the wheel?
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It doesn't say that the normal form shares the memories.
It is an attempt to make a Doctor Jekyll and Mr. Hyde character.
Seeing the above, I would say that the normal personality doesn't know what the Master Chymist does.
BTW, it is Master Chymist.
Edit:
For ease of play, it is often simpler to have the normal personality recall what he did while under the effect of the mutagen, and the prestige class description give no clear indication in one direction or the other. Ask your GM.