Hello,
1/ It’s not recommended to rename the parent theme folder. Only child theme. Child theme folder renaming is ok.
2/ You won’t face messing if deactivate and activate theme again using this https://www.awesomescreenshot.com/image/22916702?key=a057b13a19bbbcf5e0d731a4b7a075e4
3/ You don’t need deactivation anymore for the sites where I have already done that. Autoupdate should work ok in the future.
Regards