How to remove certain parts of video and corresponding audio parts from a movie

[Vesdaris]

Hey, im not sure if its the right forum but i didnt know where to post it
OK, let me explain the problem
I have a large "movie" that consists of joined small video files.
mkv,video(h264 avc), audio(AC3)
At the end of each video part there was a black screen and copyright warnings.
My question is how can i remove those certain video frames and audio parts keeping audio-video synced
What should i use and how
Thank you in advance

[[P]ako]

It'd be better if you were to encode them again. BUT, this time just by sections.