If it makes sense for a wonder that obsolete to continue functioning in a legacy kind of way after some point then it should get a legacy building that it will become upon obsoleting.
When I changed it so buildings that obsolete are removed from city, I also added a new XML tag, and code, that allows one to define a replacement building that will replace this building upon obsoletion; I made some obsolete versions of some wonders, but I figured it would be better use of my time to continue working on code rather than do XML modding which other modders are as qualified to do.
The obsolete building removal was a needed streamlining rework towards optimizing our code performance and RAM usage, it paved the way for me fixing most of the weird bugs of buildings activating/disabling unpredictably, and for the building replacement mechanic and building disabling mechanic to work in a more robust manner.
This technical change will not be reverted, as it would be extremely hard to do and would require the reintroduction of dozens of bugs that were fixed plus the reversion of perhaps 20 hours of coding work that built upon it after it was made.
If a building should not obsolete, then we don't have to obsolete it, if a building should change behaviour radically, then we can now change buidling A into B by actually using obsoletion + the new tag I added.
Example of a weird wonder that should simply disappear when it obsoletes, Leonardo's workshop.
An example of a wonder that should change behavior could be the sphinx, that obsoletes into the forgotten/buried/lost/"Myth of the " Sphinx, which again could obsolete into a Rediscovered/Excavated Sphinx. Each stage being a distinct building, only the first can ever be built, the second only give a marginal culture bonus as it is a lost world wonder, buried under sand and forgotten, a legend, the last giving large tourism bonus, and some science perhaps.
The great pyramid should obsolete at some point and become a legacy version.
First version a religious monument that also symbolizes the great power and prestige of the pharaoh of the time (political and engineering feat to marvel anyone who doubt the divinity of said pharaoh). Second stage a pure archeological (minor science boost) and tourism (cash/culture) wonder. Second stage should be a very weak wonder compared to other wonders unlocked around the time the first stage becomes the second stage (first stage obsoletes).