As I understand it, in most cases, the prints were either returned to the studio or destroyed:
Shipping prints around the country (and the world) is expensive, so it was often left to the Theaters to dispose of the prints. Some would just go out back in the dumpster, and may have been rescued by collectors, while others may have been taken by theater employees rather than being destroyed.
If you ever Google “Roddy McDowall FBI” you’ll find out just how illegal it was (and no doubt still is, at least in strictly legal terms) to be caught with prints in your house. The 35mm prints will always belong to the studios.
Obviously a few did survive, and we’re all very grateful that they did. In fact, given the red fading of the Eastman stock of hte 1960s and 1970s, even the studios were grateful that some of their prints had been rescued by collectors because without them some films may have been gone for good.