If you try to re-encode a project and you have not edited at least one of the movies in it, during the burn process you will be presented with this box:
What MEP is asking is whether it should re-encode the movies in the project. As you've noticed, encoding takes a long time and ties up your computer resources, so it is ideal if it can be avoided. That is exactly what MEP is doing.
But, what do the options mean?
The VTS_01_1.VOB is the first DVD movie file for the first movie (the next one being VTS_01_2.VOB). Fortunately, you don't have to remember which VTS is which movie, because MEP also shows your movie name.
So, if you hadn't edited that particular movie, then you would click "Use".
If you had edited that movie and it needed re-encoding, then you would click "Encode".
Similarly, if you had edited all the movies in your project, you'd click "Encode All".
So what is the "Maintain All" (or in MEP 12, "Use All") option for? Use it when you have made changes to either the chapter markers or the DVD menus. MEP will not re-encode any of your movies but will remake the DVD menus.
Lastly, what's "Rewrite chapter menu and chapter information"?
I'm not sure! But if you want MEP to remake the DVD menus again, then tick this.