No I haven't tried editing two completely separate VFAPICodec AVI files together. There's a million and one other type of permutations that can be applied and I haven't tried them all. God knows what other types of problems may be out there.
May be you should just bite the bullet and export the VFAPICodec AVI file to DV format. Then you can edit the DV format file instead. You will not loose any quality when you export to DV format. Note: This may take a while to do and the filesize will be significantly bigger.
Bear in mind that since we are fooling Premiere into doing things it's not really built for i.e. native MPEG2 editing etc, the problems you are experiencing should be expected.
Good luck!
P.S. An additional thought - instead of exporting to DV format and using up a whole lotta disc space and PC processing time, you may be able to export the timeline to DV tape. Then you can capture what you require from tape and edit as normal. Caveat - I haven't tried this and it is just a theory.
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OR just use the Sonic DVD authoring packages that support their "Open DVD" standard wich allows you to go back and edit the files already written to the disc.
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