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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.

Thank you for the reference. I completely overlooked that one.  I would  have assumed, that in the case of changes & bugfixes, the original version at least has to stay "the official" one, the one others play & rate within the rating period. But as it is written in that rule (if I understand correctly, I am no native speaker), this is not the case. You can present your changed & bugfixed version on the big stage, and just have to make sure to keep your original version somewhere in the basement, so to speak. Well, I have to remember that rule for the next Mini Jam - it makes this Jam really special.

(+1)
I would  have assumed, that in the case of changes & bugfixes, the original version at least has to stay "the official" one, the one others play & rate within the rating period. But as it is written in that rule (if I understand correctly, I am no native speaker), this is not the case. You can present your changed & bugfixed version on the big stage, and just have to make sure to keep your original version somewhere in the basement, so to speak.

Ah, my interpretation is the opposite as yours! (I am no English native speaker either, by the way. ;p)
I guess this is up to the Mini Jam bosses to enlighten us up as to how the rules should be read into!