The inter-dimensional beings who sent the species probe into John's dimension way back in
MTC will realize that of the two specimens it got, neither of them add up to a complete genetic map
of the human, so it'll send it's probe through again.
The probe, now in John's dimension again, begins wandering around the Universe until it finds
Moya again. Then, it re-enters Moya, and envelops one of the Johns. Then it calmly goes
back to it's own dimension--or the space between the dimensions, as the case may be.
The probe will seek out the first John it encountered--the one from
MTC, you know--and that's the one it'll take. The SECOND John will, therefore, be stuck on
Moya to take the place of the first John.
Meanwhile, the first John becomes a lab experiment to some inter-dimensional being (the
same one, coincedentally, from TTLG).
That's why they're showing MTC in that chain reaction in May.