I just sent my transcripts for the Jan 1st deadlines, forgetting that my school is on break and probably won’t be able to process the request until Jan 4th. Will schools still accept my application if the transcripts are late? And if they do accept it, will it being late negatively affect me? Thanks 
It’ll still be fine if your counselor uploads your transcript to Common App even a week or two after the deadline.
Wait. Is the transcript that the counselor uploads to the common app considered official? The 6th semester one.
Yes, your counselor uploads your 6th semester transcript (up to junior year) to Common App.