Now implemented a scratch filter to remove the worst of the "line drops" from the laserdisc transfer. Appears to have worked well, and in watching the new encode it doesn't look like it's adversely affected any other areas of the picture.
Unfortunately the release of this DVD has been delayed becaue I've now noticed that the audio is slightly out of sync in some areas. I didn't notice it before because the two areas I used for samples had the audio spot on. It's only very slightly out but it is noticeable and it bugs me, so it needs fixing.