Check the access rules on the missing reference. Do you have read access when you login?
We found the sollution (after quite some time) and I am still not sure if it is a bug or as by designed. We also had a module with an entity whose parent was Taak. And since this module was not selected as a module to synchronize in the MxModelreflection the parent is also not synchronized.
I am still not sure if I find this a bug. I would have found it logical it would synchronize all the references of Taak and skip the references to modules that should not be synchronised. Now it just skips all the references.
Regards,
Ronald