AA has limited interline agreements with Jetblue for certain flights to/from and between Boston and JFK. This is why they were able to "endorse" your ticket over to Jetblue to get you to JFK. AA should definitely reimburse you for Jetblue's bagge fees since, as you pointed out, if it hasd not been for their cancellation you would ahve paid nothing to check those bags with AA to be transferred to Cathay Pacific.
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