.... and that is why you should never mess with VP files unless you have a very clear understanding of what it is that you do.
What you should do is this:
1. Create a new mod folder inside your FS2 directory.
2. In that folder, create a textfile named mod.ini with the following content:
[multimod]
secondarylist = mediavps_3612;
3. Create the data folder structure inside that mod folder. This will initially consist of the following subfolders: models, maps, and tables.
4. Copy your new model to <yourmod>\data\models, its textures to <yourmod>\data\maps.
5. In <yourmod>\data\tables, create a new file named myship-shp.tbm (the -shp.tbm part is not optional). Write the following lines in it:
#Ship Classes
#End
Insert the table entry for your new ship in between the #Ship Classes and #End lines.
6. In the launcher, set your new mod folder as the active mod. Through the magic of mod.ini, your mod will now load both your mod and the mediavps.
7. Experiment to your heart's content, safe in the knowledge that you won't mess up any "official" files.
For the purpose of what I'm doing so far, which is simply to add mine and my buddie's custom ships so we can have LAN parties and blow each other up lol, its simple enough to mod my existing files.
Simple, yes, safe or a good idea, no. Look, we're pretty adamant about this whole "do not modify official files" thing for a reason. One mistake, and you screw up your install in ways that are not immediately apparent. The "make your own mod" route is easier for everyone involved, including you and your friend. Trust me on this.