I don't know why they do it.
...
Anytime the firmware updates, you need to reinstall all hacks.
The 5.6.x updates are more annoying, because you also need to update the jailbreak, see the official jailbreak thread for more details and use the hotfix listed there.
Once your jailbreak is updated, install KUAL (Kindle Unified Application Launcher) and the MrPI (MobileRead Package Installer) extension, and use that to reinstall your hacks.
Edit: Right, FGA #11:
https://www.mobileread.com/forums/showthread.php?t=237083
In fact, it is the conversation right above this one, if you look at the previous page.