if it's just the mesh and it can use the same texture, you can extract the GMDC resource from the original outfit, make a new file, import the GMDC, save the file with a new filename (don't do "Fix integrity" or other changes you'd normally do for a standalone mesh, since you want this one to replace the original). Then you can replace the mesh - you may have to do changes to group naming depending on the mesh. Make sure the new mesh can use the same texture (UVmap, same number of mesh groups/textures, etc.)
I don't even know what the "skin workshop tool" is...
For ingame meshes you can use the default database to find the name of most clothing meshes, or (if you can't find it there) make a recolor in Bodyshop and open the recolor in SimPE and check the PropertySet/MeshOverlay/TextureOverlay resource (that's the name in the "resource tree" in SimPE. The resource itself has the name you're after in the "resource view"). The first part of the name before the underscore is usually the name of the mesh, although sometimes the age or gender prefix can be different, depending on whether the mesh is used for multiple ages/genders (often the case for child/toddler or larger work outfits).
To extract the mesh you need to know the name. Usually the mesh name is something like "afbodydress" and the original recolors (the names you'll find in the PropertySets) are something like "afbodydress_blue" or "afbodydress_green"
You copy down the name before the _ and do file --> new in SimPE.
Then you find the PJSE tool (Tools --> PJSE --> Body Mesh Tool --> Extracting Stage)
Paste in the name, and click OK.
(I think you can also extract directly from a recolor file with the "browse" button, but I never do that)
Right-click the GMDC file, click "extract" (personally I tend to copy/paste the name of the mesh into the filename box, in the example here "afbodydress", otherwise you get a string of letters/numbers as a filename).
From there you can import it into Milkshape, edit, do whatever.
Or you can import it into a different file by right-clicking the GMDC in that file and replacing it.
(Personally, I like to make sure the filenames match in the file I'm in, so I copy/paste the original name so everything looks fine afterward)
Make sure to commit and save the file.