By the way i just tested it in 4.0.6 there is no way the value field set in the library is not overwritten on netlist import. Is it possible that you simply had a custom text field and did hide the value field?
I am not sure you use the term atomic correctly. An atomic part is when you have one specialized symbol for one specialized footprint (both the symbol and footprint are only intended to be used with each other. The symbol has of course the footprint pre set in the library. Normally you would then also prefill all other fields in the symbol.)
You however seem to use the generic capacitor symbol from the official library. (That would explain why the value field was pre filled with “C”)
So it might be that in the past you had a symbol for 10uF cap connected to the footprint of the 10uF cap. If you also had the value field of this specialized symbol pre filled with the same value you used in the footprint you would have never noticed that the value of the footprint is overwritten on netlist import.
Is it possible that in the past you followed the “fully specified symbol” workflow. Meaning you had one symbol per capacitor “value” that connected to its correct generic footprint? (That would make more sense. Mybe you just got confused between the roles of symbol and footprint in that particular workflow.)