I was in a similar situation and made to complete the EFT flying at UAS before going to IOT. As an unpaid direct entrant who was forced to put back his IOT entrance dates by four months because of this, it was all very annoying.
When I got to IOT I found out that others, much braver than I, when they had been told the same, told their Squadron Commanders what they could do, and thus got onto the IOT they were meant to and refreshed and completed JEFTS straight after graduation, with no ill effects on their future careers.