Absolutely agree with @gkeeth
Lots of things should be able to be done in transition.
Not allowing duplicates in the first place was a PITA that existed in DOS CAD days and should remain there.
I still remember what an abomination no duplication was, when trying to sort out gates and op-amps. 
But maybe a good idea would be to highlight this case. Not by some pop-up warning message, but for example using different color for the duplicating designators.
Thatâd be a good idea Number1. 
Not just the duplicates, but all the parts in that package.
It has been some years since I was into large scale gate swapping, but I remember asking myself, on many occasions, ânow where were the others in this package?â.
Even a schematic, with, say 3 quad opamps, it would be useful.
Edit: On second thoughts, yes, just highlight the duplicates.
Question: Is there a way to highlight all the parts of a symbol package eg. all 5 parts of an opamp symbol? I glanced through the hotkey assignment descriptions and couldnât find a way.
Ahhh, yes⌠cross probing with the PCB. 
Just a pity the highlights disappear as soon as one part is selected. 
No, definitely not!
I once had a PCB program that worked this way, and it was horrible.
Suppose that you want to swap the Refdes of U1 and U2. To do that in that program, you first had to change one of them to some unassigned number, then change the other, and as a third step change the first one again.
Humans are creative but work sloppily, and computers have no imagination but work very fast and exact according to rules (programming). And those two should amend each other. Computers should not enforce arbitrary rules that break your flow and creativity, but they should be ready to catch your mistakes and help fix them, and ERC and DRC are quite nice tools in that regard.
Clearly we differ in opinions.
I have got away with it for 30 years using EasyPC.
If I want a new package I just add one to the schematic and that works for me.
I donât know if this fits your case or not.
When I started with multiple entity parts, I made the mistake of placing only the UxA part.
Then I did a copy-paste of the UxA part and renamed it UxB etcâŚ
This does not work, it leaves Kicad not knowing which entities belong in which package.
I learned to place all entities in a particular package at once from the place part dialog.
Once you place the first entity (A) in a particular package Kicad automatically suggests placement of the (B), (C), etc⌠entity.
After I learned to place all entities in a given package at once, Kicad never had another hitch in keeping track of which entities belong in which package.
All for now
Thats exactly the way I do it.
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