Are you booking via a corporate TA? If so, I would call them up as soon as your Y ticket is ticketed (and do your research on fare difference on the particular flight combination before booking, so as to avoid nasty surprises).

I have done this with a TG flight booked via CWT with no issue - fare difference plus I think 1,000 THB change fee or so.

If booked via TG direct, I would call up to book and explain the situation - hopefully they can make it easier for you (I.e. quote you the Y fare proforma and issue a J fare directly).