[benwaggoner]

I dimly recall that Expression Encoder has the ability to append/trim multiple VC-1 sequences as long as all the picture parameters are the same. It hasn't been updated in years but I believe it is still available for download.

Adobe Premiere Pro also supported lossless VC-1 passthrough at some point, including "smart rendering" where it would reencode only GOPs that had been modified, but I have no idea if it is still supported in current versions.