PinkFlyrer,
Rules can change so my 'facts' may be out of date. When my nav course started the RAF had just stopped paying flying instructional pay. If you had been in receipt of FIP then the pay continued.
Five of my studes were chopped pilots who had all been in receipt of FIP. They continued to get it.
Two of my studes had yet to enter RAF Flying training. They had however been in receipt of flying pay in the UAS. They got FIP.
Essentially if you are getting something or if your TOS promised something (bit like pension changes) you continue to get that benefit. It is also usually your call if you want to switch to new TOS ie the new pension arrangement might be better for you than the old one.