The Russian and Bulgarian churches in the 1500s (?) and 1800s respectively declared themselves independent of C'ople with their own patriarchs and C'ople refused to recognise that, even declaring the Bulgarians schismatic until 1946. But AFAIK both were recognised by other churches in the Orthodox communion so it didn't really mean anything.
A fairly good recent example would be ROCOR. I understand that in the beginning, the 1920s, they were in communion with everybody in the Orthodox communion including C'ople. Despite hard feelings when ROCOR moved to America after World War II, coming into conflict with the existing Russian dioceses that are now the OCA (ROCOR claimed jurisdiction over them but the dioceses said no and told their people not to go to the new churches ROCOR was starting by and for the WWII Russian exiles), when SCOBA formed in America ROCOR was invited to join (it declined). But later starting around the 1970s ROCOR isolated itself from the other Orthodox but remained in communion, at least in practice, with two churches in the communion, Serbia and Jerusalem. (Meaning the clergy concelebrated.) Everybody still recognised ROCOR as Orthodox. (Even though they didn't concelebrate with each other.) So... not in communion with C'ople but in the Orthodox communion.
Also, briefly in the 1990s when there was a row over which patriarchate, Moscow or C'ople, claimed the Orthodox in Estonia (I think there was/is an exile church from Soviet times that was under the latter and they claimed jurisdiction over the mother country) the two patriarchates weren't in communion with each other, again very briefly, yet both remained in the larger communion and thus officially Orthodox.