In the posts above, Chris and I started with a recording from Fusion that would not FF or REW in MyHD, and we simply removed the first second of the recording, which resulted in a file that would FF or REW in MyHD.
In your case, it sounds like you are starting with a file that will FF and REW in MyHD, but you want to remove null packets and maintain FF and REW. To the best of my knowledge, removing null packets screws up the time base used by MyHD, so I don't think you can do this.
It would be handy to have a utility that could properly rebuild the time base. Files could be stripped of all unneeded packets before archival, and be reconstituted before playback. I know of no utility that does this.