The apt-get upgrading would only update the Kali Chroot, not NetHunter, apps, or the NetHunter kernel.
Updating from 2.0 to 3.0 can sometimes result in the NetHunter app disappearing though I'm not sure why.
I would definitely advise flashing a fresh system AND boot image at least.
After that, as long as your device has TWRP, it's as easy as flashing a NetHunter update zip from your internal storage or sdcard.
https://forums.kali.org/showthread.p...nate-installer
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