Cross posting the reply from the Github issue:
Each partition value will end up in a different Realm instance. Any relationships that you set up between the collections that fall into different Realm instances will be
null locally. If your app needs to keep references between different partitions, then you should not setup relationships and instead use the
_ids of the objects and look them up manually. Be aware though that Realm will not impose any referential guarantees there, so it’ll always be possible to end up in a situation where an object from Realm 1 points to an id that is supposed to exist in Realm 2, but doesn’t.
You can read up on how partitioning works in the docs: https://docs.mongodb.com/realm/sync/partitioning/.