Pearl wasn't "phased out" after the first season really. She wasn't talked about too much but she was mentioned from time to time and she even made a cameo in one color episode. Granny and Elly had went back to the hills and after coming back, she was seen on the phone with Pearl and Pearl was on the other end of the line, if only for a brief moment. Jethro asked Jed how they were related. Even Jed seemed confused and said something to the extent (if I'm remembering right) that his Ma & Pa were brother and sister. He ended up telling Jethro he thought he was a grand nephew, to which Jethro replied that he was a swell uncle.
As for the edits for syndication. A quick way to tell if they're edited is to look for two black bars coming from each side, meeting in the middle, and then going back out to another scene. That's the main way they did the syndication edits, although they did cut out some stuff without doing it that way. In the episode where Fairchild (the bear) eats Granny's letter from Sam Drucker, the intro to the 2nd segment gets edited out in the syndicated version. In the original version, Granny is walking up and down the front of the mansion with her shotgun calling "here, bear, come to Granny....." I didn't see any evidence of the dreaded black bar in these cuts. Yes, there were sponsor commercials in the color episodes as well. If you'll look on YouTube, there are a few spots for Corn Flakes that were done in the color years. The commercials could be every bit as funny as the episodes themselves. Also, if you can get ahold of them, the Columbia House videotapes contain unedited episodes (except for Grunion Invasion, which with a 22 minute running time is either edited or time compressed) and a few of those contain images of the sponsor of the week's product as you saw with Kelloggs and Winston in the S2 and S3 releases. I didn't see any Winston images but plenty of Kelloggs and one for LifeBuoy Soap. I haven't saw unedited episodes on TV in roughly 20 years. WREG in Memphis was the last one I know of showing them and that would've been roughly 18 or 19 years ago. I remember seeing them still on right after I got out of high school and I was injured in a car wreck the next year, which would be 1993. They had just started re-airing them in the 2AM slot at that point, starting back with episode 1. By that time, the episodes were so scratchy, grainy and washed out, they were almost non-watchable. They didn't have seasons 8 or 9 and were missing parts of season 7 as well as one episode of season 4. When the Pat Boone episode of season 7 was shown, they all of a sudden came up with crisp, new episodes of what was missing season 7, along with 8 and 9 but.....yeah, you guessed it, they were the edited versions. I've heard from Neil on here, and someone else not on here who is a fan, that Shout is looking at picking up where CBS has left off. I've even went to the point of e-mailing WGN asking them why they can't offer them unedited and what a big boon it would be for them to advertise they were showing them as they were initially shown all those years ago. I got a short, concise e-mail back saying they had no plans to ever offer the uncut versions. I've e-mailed RFD-TV (they picked up Hee Haw) and asked them about it. I got a nice e-mail back of how they'd love to pick up TBH and other rural comedies in their uncut form but it costs too much. Until Shout or MPI decide to license this the rest of the way, I'm stuck with homemade DVD's I've made from VHS.