Stephen Toub's blog has full source code to various methods for working with dvr-ms files. And can even save the closed captioning data so you can search based on dialog in the show, its all in c# .net maybe there is something in there that can help. But I think you have everything already, you already are able to strip metadata and re-insert for your other profiles. Wouldn't it be possible to just substitute the new ffmpeg generated version while your re-combining? The ffmpeg is completely standard.
On the Mediacoder, Its really cool. It's not a system, it is just a 3.5 inch little drive and plugs in to your IDE cable,and It appears to the operating system as a completely normal removable hard drive. And yes I can see it though a network if thats what you mean about unc paths.So it shares just fine.
But it isn't a disk drive. Its a special 80 gigabyte tape made for home users living room. It works really well, and somehow it pops up a directory in a few seconds after you push in a cartridge. I put the 1920x1280 HD movie "Elephants dream" on it. And it played it!. So it makes collecting shows really easy. I have cleaned off all my hard drives, and stuffed everything on a couple of these cartridges and I just point "My Videos" to it.
If your interested, the main site is at www.mediacorder-us.com. It says it can hold 200 gigabytes and it works, but thats only when the files are not already compressed which all the movies are already compressed. So just use the 80 gigabyte value which if fine for me, I already have more movies than I can keep track of on one cartridge.