Recently I was reminded of the rule that a positive commandment overrides a prohibition, and that raises the question: if the Sages can uproot a positive commandment through passive omission, then all the more so should they be able to uproot a prohibition, since a positive commandment overrides a prohibition? The question can also be asked the other way around: if the Sages cannot uproot a prohibition, then all the more so should they not be able to uproot a positive commandment through passive omission?

In addition, in the very observance of the second festival day in the Diaspora, aren’t the Sages also uprooting here the prohibition of "do not add"? And here you can’t say that they uproot it through passive omission, right?

A. This a fortiori argument can be challenged: uprooting a positive commandment is through passive omission, whereas uprooting a prohibition is through active violation. Therefore, uprooting a positive commandment is easier than uprooting a prohibition. As for a positive commandment overriding a prohibition, that is an interesting discussion in its own right (since violating a prohibition is more severe than failing to fulfill a positive commandment), but it’s hard for me to expand by email.
B. As for the question why every rabbinic enactment is not itself a violation of "do not add" or "do not subtract," Tosafot and the Rashba disagree about this in Rosh Hashanah 16b. According to most views, rabbinic enactments are excluded from violations of "do not add," because the Torah itself authorized them to do so.

As for the question whether setting aside "do not add" counts as uprooting through active violation, even though the prohibition itself is being uprooted through passive omission, I seem to recall a discussion of this by the author of Turei Even (the novellae on the Talmud by the author of the responsa Sha'agat Aryeh). If it interests you, I’ll try to look it up.