Will my re-entry permit remain valid after I apply for a Non-O visa extension?

okay, so you're going to get a single re-entry permit NOW on the 90 day Non-O visa you have so that you can come back within those 90 days and apply for the yearly extension..

When you come back, you'll be stamped in for the expiration date you have on your entry stamp of your Non-O now. Then when you get your yearly extension of stay you will apply for a new re-entry permit (which will be good for the whole year the extension is good for).. <- After you get your year extension is when you want to apply for a multiple re-entry permit.

A re-entry permit is only for the current stamp in your passport, not for future possible extensions.