SD is really old hat lately. Even if most of what you shot is SD, exporting it SD for the web isn't the best...IMHO. I've done more than a couple docs where I upscaled DV footage to HD, even though the films were 90% SD.
Here's what I suggest. Separate the SD footage from the HD in the timeline. Duplicate the timeline first..then bring all the SD footage to an upper level. Once you do that, duplicate it again, and in that duplicate, delete all the other clips from the sequence...have only SD in that timeline. Use the Media manager to COPY the clips...but trim them...and have 30-45 frame handles.
Take the resulting files into Compressor. Upscale them to 720p ProRes. Turn on the Frame controls and set them all to BEST, and DEINTERLACE. Set it up so the converted files go to another location. YOu'll have to make a custom setting for this on one clip, and apply to all. And make sure that the clip names are left alone...no added "ProRes 720p HQ" on the tail of every clip.
Now...take the SD files offline. Then relink the last sequence you made...the media managed one...to the new HD footage. They will be bigger and fill the screen, as the sequence is SD. Make a new sequence that matches the settings of these clips, then copy and paste the clips in the sequence to this new sequence. REMOVE attributes on the clips. Add the other HD footage to this by copy and pasting...keeping the same edit order. Done.
Shane
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