Hi,
You have explained that a gezeirah can remain even when the culture or the original reason has changed. Why does it remain, and how do we know which rules are formal gezeiros and which depend on whether the original concern still applies? Isn’t any rule meant to prevent an issur a gezeirah? For example, why does chicken with milk remain prohibited, while you explain that the harchakos on Yom Kippur depend on the actual concern? What in the sources establishes that distinction, and when does the rule about a beis din needing to be greater in wisdom and number apply?


There is no single rule that every rabbinic precaution intended to prevent an issur automatically has the status of a permanent gezeirah. There are several different categories, and you have to study each particular halachah to determine what Chazal actually established.
A formal דבר שבמנין is different. The Gemara in Beitzah 5a establishes:
“כל דבר שבמנין צריך מנין אחר להתירו”
If Chazal formally convened and enacted a prohibition, the prohibition does not simply disappear because its original reason later disappeared. It remains until there is a proper authority to repeal it. That is the context in which the rule of אין בית דין יכול לבטל דברי בית דין חבירו אלא אם כן גדול ממנו בחכמה ובמנין applies. The Rambam codifies this in Hilchot Mamrim 2.
Some gezeiros are even stronger. The Gemara says regarding certain established gezeiros, particularly the שמונה עשר דבר, that once their prohibition had spread throughout Israel they could not simply be abolished even by a later greater Beit Din.
But not every rabbinic rule is a formal enactment of that type.
Sometimes Chazal or the poskim give a rule because of a particular existing danger or concern, and the rule itself remains dependent upon that factual concern. A very clear example is מים מגולים. Chazal prohibited uncovered liquids because of the danger that a snake may have deposited venom in them. Yet Shulchan Aruch, Yoreh Deah 116:1, says explicitly:
“ועכשיו שאין נחשים מצויים בינינו מותר”
Today, where snakes are not commonly present, it is permitted. No later Sanhedrin had to formally repeal the prohibition, because the rule was understood as dependent upon the underlying danger.
There are many other categories as well: מנהגים, later protective practices, particular חששות, עצות, and applications of existing laws. They do not all receive the same legal force merely because their purpose is to keep someone away from an issur.
Chicken and milk is a good example of a formal rabbinic prohibition. The Gemara in Chullin 104a actually describes eating chicken with milk as:
“אכילה גופה גזירה”
The eating itself is the rabbinic gezeirah, made as a safeguard against the Torah prohibition of meat and milk. That became the accepted halachah. It therefore does not disappear merely because someone believes that today he personally will not confuse chicken with beef.
The Yom Kippur harchakot have a very different history. The prohibition of תשמיש המטה itself is part of Yom Kippur. But the additional rule about treating one’s wife like a niddah does not appear in the Gemara as a formal gezeirah enacted by a Beit Din. The Beit Yosef says:
“ומצאתי כתוב בשם ספר אגודה ליל יום הכפורים אסור ליגע באשתו כאילו היא נדה”
and the prohibition against sleeping in the same bed comes from the Hagahot Mordechai. These are later harchakot intended to prevent תשמיש, not an enactment presented in the Gemara as a דבר שבמנין.
That is why I analyze them differently. You have to ask what the source actually says, why the rule was instituted, whether it was enacted formally, whether the language makes the rule dependent upon a particular חשש, and how the Rishonim and poskim understood its force.
There is no shortcut. A rav learning a sugya has to determine what category the particular derabbanan belongs to. Sometimes it is a permanent formal gezeirah. Sometimes it is a rule whose application depends upon the continuing existence of the concern. Sometimes it is a minhag. Sometimes it is a later harchakah.
Only after determining that can you ask how the rule applies to today’s circumstances.
So the principle that a later Beit Din must be greater בחכמה ובמנין is important, but it does not mean that every precaution ever mentioned by Chazal or a later posek became an immutable gezeirah. First you have to establish that you are dealing with that type of enactment in the first place.