well, while waiting to see if the bug would be patched, I decided to go back and try some other things...since I'm not sure which thing worked, I'll just post everything I did.
I turned on my PS3 (since I had stopped playing in the hopes that a patch would be released in a few hours) and instead of loading my last save (where the confrontation with Chuck starts after what he said to Clementine) I loaded the save BEFORE that (so I had to hit the square button to "rewind") so I started off with the train being stopped to deal with Duck. After replaying that part, making all the same choices I did before, I then started out the dialogue with Chuck again. Made all the same choices there, then headed back to the train car with Clementine. This time I made all of the same choices, except I decided to cut her hair this time, then grabbed the bottle of whiskey right before leaving that train car. After doing that, and avoiding the dialogue with Ben the whole time, Lee didn't disappear this time, and I was able to successfully complete the rest of the episode.
So yeah, don't know what fixed it this time since I did a few things differently, but something made it work. The bug still needs to be fixed though, and I hope the developers are working on it. Just wanted to post again to share what I did, and to say that I was finally able to complete the episode.
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