I've had a repeated problem publishing multi-bodies. Sometime after publishing, the parts disappear from the assembly copy and they need to be re-published. An arrow appears next to the Assembly Copy title in the pathfinder.
The alert states that: " The multi-body part file this feature is referencing contains Design Bodies that have not been published. Edit the part file to publish the bodies."
Then I have to go and delete all of the named published parts, republish/re-name all of the parts. Then cross my fingers and hope they stick.