So after I posted and tagged it with 5.6.1.1 I found this thread
https://www.mobileread.com/forums/sh...d.php?t=271543 which almost answers my question with:
"you must make sure you are running the latest version of the jailbreak (1.13.N) and start using MrPI (MobileRead Package Installer) to install hacks."
My jailbreak was 1.16.N so I think I'm good there but I'm not sure how "start using MrPI (MobileRead Package Installer) to install hacks" affects my question.
Is this saying I just do the manual upgrade to 5.6.1.1 and the jailbreak will survive? and what about KUAL/KOReader? Will I have to install those again?