I don't know if you can apply cloth simulation to only part of an object (I think probably not, but I've never tried it).  If you can't, then one option would be to open the mesh in a modeling app, and split it into two files; import those into Poser, and run your simulation just against the skirt; export the results, and take them back into a modeling application again; and merge/weld them together again.  It won't be simple, but I don't think you have any easy project in front of you any way you look at it.  I think it is likely that the morphs you make will be incompatible with the old version of the skirt no matter what you do, but I've never tried any of this myself so it may be easier than I think it is.

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