You can use UVmapper. you save the uvs file of the figure. Do your thing, then load the uvs file back to the figure. It will give you all your groups back. So here are both versions of UVMapper instructions. Classic is free. This gives you a single mesh to play with then will give back your groups so you don't get that out of vert order. 

Pro version

Load the figures OBJ into UVMapper Pro
File | Export UVs ... (checking "Export Group Names" & "Export Material Names", uncheck everything else)
Select | Select Method | * by Facet
Map | Color | by Material
Select | All
Tools | Assign to | Group (and type All into the box, click OK)
Tools | Assign to | Material (and type All into the box, click OK)
File | Save Model (Leave ALL unchecked)

Classic version

The way to do this is :-
Load the figures OBJ into UVMapper.
Export the UVs (File | Export UVs ...), checking "Export Group Names", and "Export Material Names", uncheck everything else.
Edit | Select By | Facet
Edit | Select | All
Edit | Assign | to Group and type All into the box, click OK.
Edit | Assign | to Material and type All into the box, click OK.
File | Save Model, checking "Export UV Coordinates", "Export Materials", and "Export UVMapper Regions", everything else unchecked.
Be sure not to overwrite the original OBJ.

Load into modelling program and do your morphing.
Do not weld vertices or any other operation that changes the number of vertices or faces.
If the mesh isn't a unimesh you'll still have deal with the splits at group boundaries.

When you've finished your morphing, save and load the morphed OBJ back into UVMapper.
Import the UVs (File | Import UVs ...), that you saved earlier.
The grouping and materials have now been restored.
Load into Poser, then use the Group Editor to spawn props for each group, and save each morphed body part out as an OBJ so that it can
be loaded as a morph target, or use a script (see Python Scripting Forum at Renderosity) to automate most of morph creation process.