[parkher]

Ken Maltby
It is so much simpler to overwrite only the cr3 folder instead of uninstalling, installing, adding your fonts, css files and hyphen directory each time.
I just compare the content before updating:
1. I check if there are changes outside cr3 folder
2. I check if something is removed from cr3 folder that was previously there (except the stuff I added myself: fonts, css and hyphen).
So far there were no such changes.
I think this approach is very safe. If you notice such changes, maybe then you can opt to re-install everything, but even then probably you could just address those changes manually.

UPDATE: the author says, if you do not overwrite but re-install, you will lose the list of recent books, your bookmarks, etc.

I think, if you re-install, you should save your cache, bookmarks folders and cr3.ini and cr3hist.bmk files and then put them back again.