Hi NNenov,
I took some time to explore the options, and certainly not with different point counts, natively in C4D. I’m not aware if someone has created a plug in by now for that. A few weeks ago someone posted a link to algorithm that could estimate point relations even parts of the mesh of one object where gone.
I would create what you need in all “states”, then make it editable, and based on the source model (or main model) drag then all other variations into a PoseMorph. A two object (state) example is here:
Scene file
https://www.amazon.com/clouddrive/share/gjX0XCVUn69uUE9l4PmNuXp5To1cORJ52Yci17WYqCk?ref_=cd_ph_share_link_copy
Also included in this file is a suggestion to use the Smoothing Deformer to go from “hard” to “smooth” with a surface. Click on Initializing when you explore the Deformer, as after each change of segments.
Both work with PolyFX.
However, since this thread has already some length, I feel I have no idea what you really need. Let me say it in this way, I know that some projects can’t be discussed here, and some do not like to start from the beginning again. But as “framed questions” lead to limited answer, so does any question that arrives half the way. If the current state is not aligned with the shortest connection between start and target, any solution from that point will create perhaps an de-tour from no on for the whole project. I can send an upload link if the project is NDA.
All the best