I have an extension I bought that is distributed via a zip file. I installed it just fine, but shortly after they released an updated version.
I can't find any guide online for manually upgrading extensions. I would use the same process used for install, but from what i've ready I get the impression that things like DB tables might not get cleaned / updated properly if I use the exact same steps I used for install.
FYI - I looked and the extension does not include an UninstallSchema.php file, but does include an InstallSchema.php and UpdateSchema.php that I want to make sure gets ran.