Deinterlace only the frames flagged as interlaced

[Selur]

If I change the scantype to Progressive in the Deinterlace tab to disable autodeinterlace, will that custom code still work?

Why would you do that? This will only potentially cause problems.
If you load the custom code, in a custom that is inserted before the 'Deinterlace'-section the code already lets Hybrid know that the source is progressive at the end of the section. Since Hybrid knows that the source is progressive after the custom section ('# scantype progressive'), it will not try to add additional deinterlacing.
So if you tell Hybrid the source is already progressive at the beginning of the script, it will only break the preview.

Cu Selur