Doctor M said:

@Space Kaijuu,

You can use tsMuxeR to create a Blu-ray folder with the new video you want to add in. (Do the movie and short separately.) You'll want to make sure you have the same number and order of audio and subtitle tracks as well (even if you blank them later).

Under the Blu-ray tab, there is an area that says 'Options'. Here you can set the first MPLS and first M2TS. Set these numbers to correspond with numbers on the Blu-ray you are rebuilding.

Next you need to copy the .M2TS from new STREAMS folder, the .CLPI from new CLIPINF folder (will be the same number as the .M2TS), and the corresponding .MPLS from new PLAYLISTS into the old BD structure.

The .MPLS isn't usually the same number as the .M2TS and if you don't know it you can use BDEdit or various other tools to find it. (If you want info on this let me know.)

You'll also want to replace the same CLPI & MPLS files in the BACKUP folder as well.

It's... not really simple.

Bumping this quote as it contains the needed instructions.