The GET_TGT logic in v4.8 (and later) should help to avoid cross-partition links being silently dropped. However, there is still a case where the cross-partition link can be dropped.

Cross-partition links present a problem because the partition containing the link-source can be replicated before the partition containing the link-target. Historically, Samba has silently dropped these links. However, v4.8 improved things so that a hanging forward link was added.

The problem here is that if the GET_TGT flag has already been set, the hanging forward-link doesn't get added and so the link gets silently dropped.

I noticed the logic problem in the replmd_allow_missing_target() code.

If I hack the samba code to always use the GET_TGT flag, the the getncchanges test suite detects this problem.

This problem would be unlikely to affect ongoing/periodic replication, but it's possible you could hit this case when joining a new DC. 

An example of a cross-partition link is the serverReference link that gets created for DCs.