$400 dollar for a US-TYO-BKK//SIN-TYO-US flight with a stopover in Japan is not unheard of. Cheap yes, but does not need to be a mistake fare.

I guess the PL email received 3 days prior to departure was the autogenerated email that everyone with a PL itinerary receives. I suspect that this email may be sent out based on initial booking details without taking any subsequent changes into account. But yes, it certainly lead to an expectation that the pax were good to go/travel.

Refund: If JAL mentioned refund it would a refund to PL rather than the OP/pax. So it may be that JAL has cancelled and made a refund to PL but PL failed to notify the pax and to process the refund of the fare amounts paid.

In any case, you need to take this up with PL as PL is responsible OTA/party and needs to rectify this if a mistake has been made on their part. I doubt JAL unilaterally decided to cancel the tickets.