You are right Thunderbird, but I have modified the rules-as-written somewhat. From the House Rules thread:
The Shadow:
Alpha Flux
Happens a lot less frequently than the rules as written. Each district of the city gives a chance per day of Alpha flux occurring.
Alpha flux is a painful process, taking 6 hours while one mutation recedes and another takes its place. During these six hours:
- neither the old or the new Alpha power can be used.
- you are Weakened.
You no longer experience Alpha flux on rolling a natural one.
Alpha flux that takes place during combat can only occur once during a given encounter. The above effects start at the end of the end of the encounter. Until then you may use your old power.
Alpha flux automatically occurs when the you rest up in Compton between expeditions.
I just found constantly shifting decks of mutations to be too gonzo (even for me Arcus!), plus the admin would be a pain. Also, the rule about rolling for Alpha flux mid-adventure I have honoured, like the bard said, more in the breach than the observance.
Perhaps I would use them if people were spamming overpowered mutations, but so far that hasn't happened -everyone has been very restrained. That said, in the circumstances spamming Body of Light will be just fine :)