The likely reason is a defective LTE modem (board) or PCIe ports on the board, or maybe all of them.
most likely it's the modem. i also encountered one (inside a LTAP mini) which was working fine (indoors) but stopped, and on the next reboot the LTE interface was gone.
if i do an usb power reset to the modem slot, briefly it is detect as MARVELL WUKONG, then it disappears for good. also tried to test the same modem with a regular PC (using an USB-to-mPCIe adapter) and it didn't work there either.
i replaced the modem with another R11e-LTE, and the LTAP is working fine again.
the issue was not related to any firmware upgrade events. though.