It is not possible to increase teh single EP FIFO size to greater than 2k in FX2LP. You may consider FX3/ USB 2.0 counter parts of FX3.
You can keep your endpoint as an ischronous endpoint and configure EP2 in 1024 x 4 buffer size. This corresponds to mode 12 of the EZ-USB endpoint buffer configuration. Refer Figure 1-17 EZ-USB Endpoint Buffers of the EZ-USB Technical Reference Manual.
This might be able to solve the problem.
Another way to do it to use the Asynchronous mode of acquiring data in the host application. You can see that the Streamer example application provided with SuiteUSB 3.4.7 is an example of how to achieve maximum throughput from the host side.
This way you can take maximum advantage of the USB host and achieve higher throughput.
You can in fact check your device (fx2lp+sensor) with the streamer application and see if you are loosing any data then.