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I cannot give you advise beyond pointing out a general feature of Geant4; e.g. the user cannot change properties of the track from SteppingAction. If you want to change anything about the track you have to write a 'process' in the spirit of G4. This process can then propose a 'particle change' object. How this works in detail has been presented at tutorials and I encourage you to search the agendas and presentations.
I found this was a good presentation at the time - now quite a few years ago.
There have been some design changes since with the G4ParticleChange class and some method names have changed. Therefore, its a good idea to crosscheck with current code. For example, a very minimalistic process code is G4OpAbsorption. (in source/processes/optical):
This shows you how to implement the GetMeanFreePath and a simple DoIt-Method.
That said, I don't know how you can change the excitation energy of an Ion, except as you say, when it is instantiated. Of course, with a process you have the option to kill the original ion and make a secondary new ion with a different excitation energy.
Your question can perhaps better be answered by someone monitoring the 'hadronic forum'.