Okay, I think I've got it all figured out:
1960
Hanna-Barbera produces "Rise and Shine" opening and closing titles in color for The Flintstones. Color negative and one color print put in a vault
Opening and closing titles made in black-and-white for each episode, with sponsor plugs, because ABC hasn't begun color yet. Network is provided with one 35mm and one 16mm standby print (some of these end up in the hands of collectors)
1962
"Meet the Flintstones" opening and closing titles made. Sequences are updated twice, once to add Pebbles, and later to add the Rubbles
1965
Alternate close appears, with Pebbles and Bamm Bamm singing (reprising sequence from "No Biz Like Show Biz")
1966
Show ends its ABC run and reruns go into syndication. "Meet the Flintstones" open and close are put onto episodes from first two seasons, meaning the credits no longer match the episode. At the same time, "Copyright 1966 Hanna-Barbera Productions" added to the open
20 first-season episodes are withheld from syndication, and provided to NBC for a Saturday morning run. The line "Through the courtesy of Fred's two feet" is edited out of the open, so when the song ends, there is time to add a voiceover, to the effect of "The Flintstones, brought to you by..."
1967
Saturday morning run ends. The 20 episodes are added to the syndie package, with the voiceover muted out... the edit, however, remains. These syndie prints continue to circulate for the next two decades
Late 80's
New prints are distrbuted by Worldvision Enterprises (sister company to H-B under the corporate umbrella of Taft Broadcasting). Unedited "Meet the Flintstones" open is restored. However, the closing credits no longer match on ANY episodes. Some opening tags are lost, and in a few cases, re-created by taking a scene from later in the episode and editing it onto the open
Mid 90's
Laserdisc release is announced. Search begins for any lost footage, hoping against hope to find "Rise and Shine" open and close in color.
Eureka! Color negatives and one print each of original open and close are found in a Turner facility in Hollywood. These have never aired
Laserdisc box set of partial first season is released. "Rise and Shine" open and close is restored, and seen in color for the very first time. Because the color negative of the close contains no actual credits, these are re-created, matching the original typeface as closely as possible, and including as many first-season names as is practical so that single set of credits can be used on all episodes.
Restored episodes also appear on Cartoon Network (and later Boomerang). These, however, are missing the "ABC Television Network" plug at end, replaced by updated H-B and Turner logos
2004
Season one released, in its entirety, on DVD. These episodes are restored as they appear on CN/Boomerang.
Whew!
I am such a loser.