when you say “some geo” is missing, are you saying that the actual geometry is gone, or that it just doesn’t render anymore? (ie: can you still see its wireframe? From what you describe with your undo operation, I am guessing that’s your case)
typically, we’ve had to deal with issues like that randomly here as well.
When the geometry was actually gone, it was most generally caused by some #IND or #QNAN in the .ma file that was invalidating this particular object (float precision issues when serialized as text).
Quite simple to fix by replacing all occurences of #IND and #QNAN by zeros, save the .ma and it should fix the missing objects.
If you can still see the wireframe, but no shading, it’s mostly some retarded issue in how the graph networks of groupId and instObjGroups attributes update. You’re in to reassign the materials by hand eventually.
I had this issue tracked by a support ticket at Autodesk and given them a scene of ours and I am not really sure if that lead to any development/bug fix on their end. Hopefully in 2013?
if It’s neither of these, then disregard the above
Also, when you’re talking about multiple shapes under a transform, are only one of these not greyed out in the hypergraph? To our experience, these seems to be created somewhere during the life cycle and modeling operations on the object. They seem to be harmless and just some carried over cached data of some sort. I used to delete them by hand with no effect when finding them (after making sure they were not supposed to be there).
They seem also transparent to most python commands operating on mesh shapes except to some advanced API based scene parsing stuff.
So far, I haven’t found them to have any ill effects to our exported data. YMMV though.