Проблем не будет, есть автобусы между терминалами, багаж перевезут:
http://flydubai.com/english/booking-wit ... .aspx#2579 If you want to transfer in Dubai to or from a flydubai flight, you'll need to make two separate bookings: one on flydubai and one on another airline. The flight you book to Dubai needs to arrive at least 3 hours before the scheduled departure of the second flight. If you don't have a UAE visa, the scheduled departure of the second flight needs to be within 24 hours of your arrival in Dubai. Without a UAE visa, you will not be allowed to leave the airport.
When you reach Dubai, you'll need to go directly to the Dnata transfer desk (before immigration and the transfer security point) where you'll be checked-in for your next flight and your bags will be re-tagged for your final destination. You'll be asked to present the following documents:
your confirmed onward ticket or flydubai booking confirmation
valid travel documents for acceptance at your final destination
your baggage tag - if you checked-in baggage at the start of your journey
If your baggage is oversize and/or overweight, you'll need to pay the relevant excess baggage charges at the transfer desk.
You'll then continue through security to the departure gate. Buses will be available to Terminals 1, 2 and 3.