Will changes made be gone with theme upgrade?

Hi

I need to know if I make small useability changes to the theme, like for example add more instructions on the registration page to help users register easier, and I then upgrade to a new version of the theme, will these changes be lost?

Also, my structure will be as follows, Wordpress MU enabled installed on my maindomain.com and I will create a domain within my MU installation for my buddypress maindomain.com/community and then point my buddypress to this domain, I will follow these instructions:

http://codex.buddypress.org/getting-started/install-buddypress-on-a-secondary-blog/

Before I do this, I might as well ask, is buddypress multi site aware yet? If so, how do I enable this? If not and I do install buddypress on a secondary blog in my network, will the edu theme still work?

Thanks!