Firmware udpate resets everything

HI

I am new to modding. I have a clara hd and wanted some guidance on how to stop firmware updates from removing koreader.

I am using this guide to install koreader but everytime a firmware update comes my whole setup disapears.

https://www.mobileread.com/forums/sh...d.php?t=314220

Another question i have is the patching threads in the developer corner like the one below . what do they patch exactly how are they useful?

https://www.mobileread.com/forums/sh...d.php?t=332469