You can have two visas overlapping but you need to enter and exit Turkey on the same visa so make sure she enters on the one that will be current on exiting.
Remember the 90 day thing is counted backwards from your departure day but if she is planning to stay until May the September trip will no longer count...
If she overstays at all expect a fine and a trip to the “visa violation” kiosk which husband had to do last year at Istanbul...