www.makemkv.com

So I have multiple Shonen Jump Blurays where they put most of the episodes on a disc into one 2 hour long file. So when I rip the disc is there an easy way to separate them or am I fucked?

Most Season Blu-rays have one Title (MPLS Playlist) which combines all Episodes on this disc (big size ~30-40GB). But there are normaly also Titles (MPLS Playlists) for each single Eposide (small Size ~10GB).

If the discs are authored with one, big title, mkvtoolnix will let you split on chapter/time boundaries. You'll need to figure out where the splits happen, but the tool does what you need.

Of course, if you process them with handbrake, you can split the episodes out AND have about a 75-80% reduction in the space taken up by the video, without noticeable degradation. Anime compresses VERY well.