Capture from the LD source at full resolution without cropping. Make sure "top field first" is selected. You must have zero dropped frames.
In VDubMod: Video > Framerate > inverse telecine - Choose "reconstruct from fields - manual" and in the offset box put 3.
Start your video on the first progressive frame of the sequence (P P P I I).
Crop/Filter/Do whatever else.
Try this on a short clip first to make sure you have all the settings right. Not once have I found an extra interlaced frame in my video after this. The only thing I can't answer is whether any progressive frames are lost.