Picofly doesn't decide whether its boot to sysNAND or emuNAND.
Picofly jobs only modify the boot sequence such that it will load payload.bin on the microsd. Thats all.
Its hekate (that usually use as the payload.bin) which responsible on booting to sysNAND or emuNAND. My guess is the hos in the emmc is corrupted, thats why it couldn't boot. Or wrong fuse count number. Or less probable scenario, wrong hekate configuration.
What is IMPORTANT for you to do first is backup your raw emmc then backup the key (prodkey, etc), its unique on your device. If you lose these key, your only option is use the shared key on the internet which is a banned one (you can't use nintendo shop, etc).
I think the safest advise i could give is try to reinstall the hekate on different microsd.
Use this
https://rentry.org/SwitchHackingIsEasy as reference.
The other option like rebuild the hos, or install the atmosphere to sysnand, or update the fuse count, all have risk of breaking your system, and need further advance method to solve.
DONT try to update your picoly firmware.
It might break, and you need to take out the picofly and reupload the firmware, if it did break. Taking out the picofly is not as easy as it seems to. You might break the pad, and the solution will be like hell difficult.