From 1959 until 1970 Bonanza was filmed at Paramount. "Virginia City" was the set used for "Tombstone" in Gunfight at the O. K. Corral. From 1970 to the end early 1973 it was made at Warners/Burbank. This is where most of the "lost" episodes originate from and I always thought the studio change had something to do with that as each studio might have negotiated separate syndication packages.
Are you sure they moved to Warners?
The 'lost' episodes are the ones that were left out of the original syndication package. The reason they picked certain episodes and left out others had nothing to do with switching to a different filming location. They wanted to syndicate all the ones with Pernell Roberts, because viewers usually remembered Adam having three grown sons (Adam adopted teenager Jamie in the later seasons). And also when they started syndicating them, the show was still in production-- so it was easier to rerun the ones from the early seasons which they called 'Ponderosa' to differentiate them from the later ones that were still being made under the name 'Bonanza.'
When NBC cancelled the series in early 1973, the 'Ponderosa' package reverted back to the original 'Bonanza' title, and all the later episodes that were not in the original syndication package just were never broadcast again. That is, until the late 80s/early 90s when Pat Robertson's Christian Broadcast Network wanted to air them, and Paramount created the second syndication package which it titled 'Bonanza: The Lost Episodes.'
Incidentally, Pat Robertson found several of the 'Lost' episodes objectionable and anti-Christian. There were maybe two or three 'lost' episodes that stayed lost, because Robertson wouldn't run them-- one was about a woman who had psychic visions, and the townsfolk believed she was a witch (played by Louise Sorel).
But in 2012, when the Encore Westerns Channel brought them back to television, the ones Robertson didn't air were finally shown again, and those had not been seen since the original NBC telecasts from the late 60s/early 70s.