This is one of the major change points in Dr Who history. First, of course, we change from Patrick Troughton, the second doctor, to Jon Pertwee, the third, We understand that was at Patrick Troughton's request, but why get rid of the second doctor's two companions, Jamie and Zoe? Did they request to leave the show as well? There's no record of that I've come across so far, if I find one I'll post it here.
Doing a table like this it's just depressing and disgusting to see all the MIA episodes in the Patrick Troughton years, and looking forward into the Jon Pertwee years seems odd because there are no MIAs at all! So what happened here? Did the BBC realize they were slaughtering someone's art? Doubtful. Did they realize that they had a popular show on their hands that might be valuable in the future? Maybe, but then was it just a coincidence that it happened at the same time as all these other things? Maybe it was part of Jon Pertwee's contract. Or maybe it had to do with...
...their switching from black and white to color. Maybe the old Patrick Troughton tapes couldn't be used to record color shows and that's the only reason there are any Patrick Troughton shows left.
Another annoying point about the re-writes of old Patrick Troughton tapes is the randomness of it. If they had just decided to eliminate whole stories instead of grabbing episodes from almost every story, a lot more complete stories would have survived.