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Hi @e_frissell. This may be because of ModelStates. If the lower level model document had more than just the one original ModelState, then the changes at that level may have been recorded by a different ModelState than what the assembly component in the assembly is set to. Or, the sub assembly that the lower level sub assembly/part was put into as a component, may have more than one ModelState, and the ModelState of the component was set differently in one sub assembly level ModelState vs the other. This can be difficult to weed out. ModelStates need to be set-up from lowest level to next level, to highest level, in that order, or top level stuff may not be seeing the lowest level stuff properly.
Below are just links to the online help documentation pages for the 2 update methods, and 2 rebuild methods, for others to reference.
Wesley Crihfield
(Not an Autodesk Employee)