For whatever reason, my phone was in the same situation as yours where I could only reboot into twrp. I found a pretty easy solution below:
before trying anything else just type in these commands
What worked for me was from the TWRP terminal command was to type
dd if=/dev/zero of=/dev/block/platform/msm_sdcc.1/by-name/fota
then hit enter
dd if=/dev/zero of=/dev/block/platform/msm_sdcc.1/by-name/misc
then hit enter and reboot.
got help from the IRC xda-devs for the second step to complete the fix.
It worked for me and now my phone seems to be running normal. The whole thread is located here:
I think my phone somehow took the OTA while I had KK rooted installed. I plugged in my device to charge and got up to get a drink and when I came back my friend's cat was playing with the charger cable and my phone was in twrp. Went the whole weekend on vacation without my phone. It was rough. All seems well now.
Edit: I think I had to enter everything in twice. 1st time it worked but then rebooted back into twrp on it's own, the 2nd time it worked. Hope it helps.