Hi @alfredogzz,
welcome to the Plugin Cafe forum and the Cinema 4D development community! Please have a look at our Forum Guidelines as we have to ask all users to flag their questions with tags. I have added a Python tag (assuming that is the programming environment you are after) to your posting for you, but you have still to add an OS and Cinema 4D version tag yourself. Please also note that providing full solutions is outside of the scope of support (see Forum Guidelines), so it would be best if you could post whatever code you already have.
About your problem, let's assume you have an object Obj which has has the "incorrect" c4d.Matrix, i.e., transform, M_old and you want to move that transform to the known transform M_new. Let's also assume that all our transforms are in global space.
What you basically have to do is:
Compute a difference matrix M_dif for M_old and M_new. One way to do it, is to multiply M_new by the inverse of M_old, i.e., "untransform" M_new by the amount of M_old. Multiply all vertices of Obj by the inverse of M_dif. Set the global matrix of O to M_new.Here are some other postings, topics and examples (the first one contains code for pretty much what you want to do) that might be helpful for you regarding this topic:
"Move" the transform of a point object
Setting coordinates for selected faces (Python - Beginner)
Mirroring with Matching or Different Axes
If you import your geometry from Rhino, you might also have to deal with baked normals, i.e., normal tags. Please take a look at this thread for that scenario.
It also noteworthy that Rhino's coordinate system is right-handed with Z being up, while Cinema 4D's system is left-handed with Y being up. Handedness of coordinate systems has been discussed in Mirroring with Matching or Different Axes for example.
Cheers,
Ferdinand