I am a bit confused by Mystic Subdual. I assume that if a creature enchanted by this had any keyword tokens on it, those keywords would no longer apply to the creature though the tokens would still remain on the creature? What would then happen if a second identical keyword token were placed on the creature? Would it then gain the ability from the second token, or not?
After Mystic Subdual is attached to a creature, that creature can still gain abilities by new effects, including by new keyword counters (not: keyword tokens [C.R. 122.1]) given to the creature, due to the "timestamp order" rules (C.R. 613.7). If the creature is given a new flying counter (or a spell, activated ability, or triggered ability gives it flying) after Mystic Subdual is attached to that creature, it will regain flying; in the case of flying counters, this is because all flying counters on an object receive a new timestamp once a new flying counter is put on that object (C.R. 613.1f, 613.7, 613.7a, 613.7c, 613.7e, 122.1b).
Although this may be in conflict with what Mystic Subdual's reminder text says, remember that reminder text "has no game function" and is not necessarily as rigorous as the comprehensive rules (C.R. 207.2, 207.2a). Mystic Subdual says the "[e]nchanted creature ... loses all abilities", so it behaves no differently from most other effects that say certain permanents "los[e]" certain abilities, such as found in Blood Sun or Humility (but compare Mystic Subdual with Archetype of Imagination, whose rules text includes "can't have ... flying" which is not reminder text and has a special meaning in the rules [C.R. 113.11, 207.1, 207.2, 207.2a]).
Note that effects that take away abilities from a permanent don't remove any counters on that permanent, whether they're keyword counters or not.
Although this may be in conflict with what Mystic Subdual's reminder text says, remember that reminder text "has no game function" and is not necessarily as rigorous as the comprehensive rules (C.R. 207.2, 207.2a). Mystic Subdual says the "[e]nchanted creature ... loses all abilities", so it behaves no differently from most other effects that say certain permanents "los[e]" certain abilities, such as found in Blood Sun or Humility (but compare Mystic Subdual with Archetype of Imagination, whose rules text includes "can't have ... flying" which is not reminder text and has a special meaning in the rules [C.R. 113.11, 207.1, 207.2, 207.2a]).
Note that effects that take away abilities from a permanent don't remove any counters on that permanent, whether they're keyword counters or not.