Is it a semi-transparent logo? I developed an AviSynth script for the Rad source that was fairly successful:
http://originaltrilogy.com/forum/topic.cfm/Rad-Helltrack-Edition-Now-Available/post/425964/#TopicPost425964
Solid logos are more difficult, but if you have a logo-less DVD, and it matches up frame-for-frame with the HD source, then you should be able to upscale that portion and overlay it over the logo.