Hello claysp5bg,
Thank you for your question regarding copying active sites back into staging. Taking the questions in reverse order, the Save & Publish button in active or staging means that the changes are saved and published in whichever environment you’re working in. That is the only way to save. If you want to put the active site back into staging then you can do so by clicking the “Deploy Staging” button under the Customize menu. This basically reverses active and staging so that whatever was in staging becomes active and whatever was in active goes back to staging.
Considering your concern about the old theme that returned, are you asking if the Save & Publish button may have triggered the unintended effect of bringing back an old theme? If that is the case, then it would certainly be an unintended effect, and it is not something we have experienced. However, if that is the case then I would be interested in replicating it. If you have any steps, links, or screenshots that might demonstrate the replication please feel free to provide them.
Best,
Christopher M.