They both are expressions that name rappers songs.
I have intuitions, but what exactly do they mean?
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According to the rap exegesis site Rap Genius, the title phrase of Wu-Tang Clan's "Protect Ya Neck" in context should be taken as a threat to the person/party the song is addressed to, with the implication that the rapper or someone is about to try to chop off the addressee's head. It means something like "en garde" or "put your dukes up".
Meanwhile, it proposes here that in Busta Rhymes' "Break Ya Neck", the titular phrase is an exhortation to the listener to nod vigorously along with the rap very hard -- it's a hyperbole, to bounce one's head with the beat so hard as to break one's neck.
Ya is a slang term. I've often heard ya where they want to use your. The commonest, though offensive, is 'f*** ya a**!' means 'f*** your a**!'
I listened to those song and it's full of slang words it seems. This backs my answer!
Protect Ya Neck and Break Ya Neck, in that sense, could mean 'Protect your neck' and 'Break your neck'. And yes, listen to the video Break Ya Neck, the singer sings *Break your f*** neck!*
The OnlineSlangDictionary defines your as one of the meanings of the slang term ya.