Actually have a third question also. Read in a local pool forum that phmb decomposes to ammonia and urea and that the later is something you want to avoid in your pool. No idea if the guy knew what he was talking about. But it made think a bit about whether there are any health aspects to the conversion. Anyone who knows more about that?
I'm not familiar with the chemistry around phmb. But if it does decompose to ammonia and urea, then chlorine will take care of them. Both create a massive chlorine demand.
There are scenarios where (if FC had been allowed to drop to zero for long periods, e.g. when closing the pool over winter) certain soil bacteria can decompose CYA into ammonia. In these instances, you can pour litres and litres of chlorine into the pool, and FC will not rise. Until you used enough chlorine to decompose all the ammonia, and then FC will start to hold again.
Some of the chloramines (or "combined chlorine" aka CC) that get created along the breakdown process of ammonia and urea are what most people associate with "chlorine smell" in public pools (particularly indoor pools). They are unpleasant and in high concentrations not exactly healthy. But you are not using your pool during the baqua conversion process and it is well ventilated, as long as you keep those nifty glass panels you have open enough to get some ventilation. I don't see an issue there.
Once you'll have completed the baqua conversion, you'll be maintaining your free chlorine levels according to TFP's FC/CYA chart. As long as there is sufficient FC at all times, CC gets broken down continuously as it gets created (e.g. from nitrogen compounds in swimmer's sweat or should a child be too excited by all the pool business to go to the toilet, or from algae being killed), so chloramines should never build up in significant concentrations.
A properly maintained pool (i.e. with sufficient FC according to the FC/CYA chart) should have no "chlorine smell". But you should open your panels regularly to let any breakdown-product built-up breath off.
There is some information on ammonia (in regards to the above mentioned CYA decomposition) in the TFP wiki:
www.troublefreepool.com
There is also some info on combined chlorine:
www.troublefreepool.com