You seem to be thinking of something else where the word "evolution" does not readily apply. That word generally means a gradual change, in particular in response to environmental triggers, mostly in biology yeah but not exclusively - like political thinking "evolves" over time. Atoms gaining/losing electrons or even protons/neutrons is rather sudden, and while I suppose you could model the total number of subatomic particles in a system and use the atomic configurations they are in as the "identity" state that "changes" over time, or in response to variations in a star let's say, or even more loosely the amount of time that they bother to form atoms at all in such a plasma state, but I have never heard it used that way.

Maybe an example is how a computer is not only made up of 0s and 1s, but a system that makes use of those 0s and 1s to accomplish tasks, so that it is not merely flipping bits for their own sake, but instead, changing the bits alters the actual "information" content present in that system. It is the information itself then that evolves, not merely the bits, nor the electrons that make them up. In contrast, if an animal grabs ahold of a computer's hard drive, it may nibble on it, bat it around, try to mate with it, use it for nesting material, etc., but absent the computer itself, the patterns of 0s and 1s and electrons and such is no longer relevant. Hence even if it changes e.g. gets erased, or constantly gets modified by irradiation or whatever, I think we would no longer call that "evolution", even though it is still "change". Ideas likewise can evolve bc we humans will adapt our actions based off of those thoughts, so the patterns are still part of an "information" system.

But subatomic particles being in an atom or not... I don't see how that stores any "information" really, at that same level of organization. I mean it obviously does, bc everything is relevant, but what is interesting about it? Rather, atoms form the substrate building blocks upon which other forms of computation can take place, and like while biological DNA cannot store information without its component atomic structure, at the end of the day it is the "information" present in the DNA that it said to evolve, independently of its origin. Proof of that comes from us now being able to synthesize completely artificial DNA from scratch, using whatever code we input into it - so despite having no physical connection whatsoever to the original, a genetic message can be replicated, with or without modification. "Descent with modification" can now happen to messages that once were purely biological (as far as we knew, absent any aliens that originally made it or our computations all being a simulation in The Matrix or some such:-) but now can go through a virtual phase.

In contrast, while atomic structure certainly "changes", I am not aware of any information processing systems that really make use of that fact, beyond the obvious "atom A is over here and like this, while atom B is over there and looks like that". Then again, who knows really!? Anything is possible!! As the quote from Chrono Trigger says:

Am I a butterfly dreaming I'm a man... Or a bowling ball dreaming I'm a plate of sashimi? Never assume that what you see and feel is real!