Long ago I also had the same problem with the USB menu not being displayed in my LP SE II; however, I could solve it. In your case I'd try to apply the latest available USB F/W which is applicable to your particular Phatty model.
How to do that? Without entering any Phatty menu, just connect the MIDI cable (preferrably try a "USB-to-DIN" cable first) between your PC and your Phatty, start any application that can handle SYX files and transmit the proper USB F/W directly to your device. In fact, the F/W is made of a simple SYX file which should be recognized by the LP or SP without any additional intervention (if you're using the latest main F/W as well). Here are the links to the mentioned USB F/W from Moog support (and those links still work):
LP USB Firmware (V33):
https://drive.google.com/open?id=1-QsDk ... 8FzxJ6wiGo
SP USB Firmware (V34):
http://www.moogconnect.net/downloads/ph ... SB_v34.zip
Caution: Only apply the proper USB F/W to the device you really own. Don't mix up "LP" and "SP" USB F/W versions!
As mentioned before, personally I'd also recommend to update to the latest main F/W 3.21 (with the latest build applicable to your device) first, even though other people reported that they have bricked their device. The main problem seems to be that no one reads the enclosed Moog instructions. Some users seem to have skipped the important step to apply a particular F/W update in between which is providing a new bootloader. After that, the latest main F/W 3.21 may be safely applied. At least I didn't have any problems by doing so. Again, please read the instructions carefully and you can't go wrong. Always reboot your device after each upgrade step. The "USB/DIN" entries should now be available again as MIDI options; the new F/W info (for both, main load/build version and USB version) can also be looked up in the related "System Utilities" menu.
Hope that helps. Good luck.