Just wanted to let you know that I narrowed down the specific resource that doesn't transfer correctly (for hairs at least).
In Milkshape, it's the Comment entry listed as 'EmbeddedLong002'. Unfortunately, I don't know what the equivalent of this is in S3PE's preview of the GEOM data.

The preview of a GEOM in S3PE that was exported with this tool gives shows a 'Error reading resource' log. I know this can happen to resources that are perfectly functional, but being able to preview and edit these further in S3PE is quite valuable.
Opening both the reference and the new export in Milkshape reveals that the only Comment that isn't identical is the entry for EmbeddedLong002.
This is the case even for an unedited EA geom imported and immediately exported. Replacing this value with the one on the reference fixes the S3PE import/replace issue.

Thank you greatly for sharing this tool. All things considered this is a pretty trivial hiccup, the process for refitting meshes is still better than ever.

Edit: Adding as an edit so I don't clutter the comments- it is the MTNF entries that are broken on export and it can be fixed with Delphy's SimGeom editor instead of Milkshape. There isn't an obvious disparity in the MTNF details, but exporting it from the reference and importing into the new GEOM fixes the 002 entry.
I was also wrong about Extra Data Tool, TagVals are assigned on export- they just don't show in MS.

Hello! Can you explain how to assign the vertex groups to the imported rig? I'm having a hard time trying to figure that out (even though it could be right there in my face haha).