According to the rules, as long as the new versions stay separate from the original one, this is fine. I think this means the original one should be evaluated. I don’t know how the two games you mention dealt with it, but if you feel they drifted away from the recommendation, I guess you can still tell them to put the original version in plain view and to clearly state which version is which.
Can I make changes during the rating period? Yes, just make sure that the original version of the jam can still be downloaded.