Hmm... What version of LW? I think this is a known bug in 8.0. There's a number of ways you can work around it.
The first is to simply copy the entire object, layer by layer into another one and save... tedious, and you might miss something such as maps, etc... but works.
Another option to try is to run modeller without the hub (don't know how to do this on the Mac - on a PC add the switch '-0' (that's zero) to the command line)
Hope this helps...
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