In fact, it is purely additive process: we iteratively add the most frequent pairs to the set, until we reach the desired total number of tokens. But we never remove tokens, we keep everything, including the initial 256 tokens, representing bytes.
This ensures that the model is capable of producing every possible unicode sequence (in fact, I think that it is capable of producing every possible byte sequence, but bytes that are not valid unicode are filtered during sampling).
Edit #1: also, this page entirely skips the attention mechanism, which is, in my opinion, both the most interesting part and the part that is hardest to understand (I can't say that I fully understand it, to me it is just some linear algebra matrix multiplication magic).