Full flag will not be a problem for you if you are using two GPIF II threads to get data into FX3 and if PC can match the input data rate.
You can refer to AN75779 for two thread implementation. But if you are BULK transfers then there can be a case where your DMA buffers get filled with data and waiting for IN requests from PC host. There you can not avaoid this full flag problem.
Please let me know if you have any more questions on this.