Richard the ph of the detergent affects the bonding of the protector, a slight acidicness left on the fibre probably around the 6 to 6.5 is the best for most water based protectors. The higher ph will kill the affectiveness of the protector.
As for chemical left in the fibre I guess it depends on how much is left in, the florocarbon will not be able to enter if the fibre is 'full' but other protectors like gardsman protect around the outside of the fibre so I don't think that is so much a problem.
Gardsman is from what I remember a solvent/silcone product and as the industry goes means that it's protecting qualities are not as good as water based.
Shaun