That guide is for the most adventurous ones but it doesn't answer my question.

If you just keep Phoenix installed, you should be able to even get updates from Google Play and if not, updating from a direct download should be safer than to remove Phoenix, first.

If you want to continue using Phoenix, removing it is definitely the wrong choice.

The Play Store app would let you uninstall side-loaded apps and if they are signed by the same keys, you could even update side-loaded apps from Google Play. Uninstalling to install from GitHub makes no sense at all unless they signed with a different key.

If you uninstall, you risk to lose funds and you inevitably end up incurring on-chain fees.