Do the dvds play at all now that they are edited? I mean, have you tried them in an alternate player like Media Player Classic Home Cinema or VLC?
If you can play them in one of those software players, you might be able to salvage them using other tools, and get something that will work in Windows Media Center.
Personally, I'd demux the audio and video and use my dvd authoring program. But it isn't free.
There are alternatives if you don't mind losing the original menu, and if these edited dvds actually play in something. Let us know and we can probably walk you through reauthoring them.