You can break it into multiple files and adjust the cropping for each file, then at the end, use tsmuxer to append them together. By the way, I used tsmuxer to convert the .mkv to AVCHD which is what I posted in the link above.

Edit: After thinking about it, I am not sure how stable that break in the encoded files would be. Two other options would be to crop each file and resize inside of VirtualDub, save as lossless AVI, then join all of them together into one AVI when all the files are the same resolution. Then use Xvid4PSP to add the black bars and encode. The other option would be to crop the files in VirtualDub and try to join them in Xvid4PSP. I am not sure how well it handles files of different sizes though, so using Virtualdub is probably the best option.