You don't seem to understand what linux from scratch is about, it's about building (compiling) a linux installation from scratch, basically without a package manager, one by one.
As you don't really understand what you're attempting, some brief answers:
- yes you may destroy part of or your complete system
- if you replace parts of your system there may be security consequences
- you should not try this on your main system, obviously, and no there is no easy failsafe way
- for your question about snapshot/timeshift you should start a separate thread
To build a newer version of gnupg you only need to build that, and the libraries it requires if those are required in a newer version than what is available.
If you want to try that, it's probably easier to rebuild a src.rpm from cauldron, where that newer gnupg version is already present.
I've described this here:
https://forums.mageia.org/en/viewtopic.php?t=5530Although you don't mention WHY you want the newest version of gnupg in the first place.