FX3 <--> USB Connector schematic line is below right?
You can swap the SSRX pairs. This is because, during SuperSpeed enumeration, certain training sequences (called TSEQs) are sent and the D10.2 symbol in this is used to detect if lane polarity inversion is done (refer to section 6.4.2 of the USB 3.0 spec). However, such lane inversion detection is not done in USB 2.0 enumeration.
So, this is okay. This inversion is recommended if your design will cause SSTX+ and SSTX- (or the RX pairs) to cross each other. Then you can swap these pins to avoid this crossing.
I changed the SSTX+ and SSTX- signal.