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If you still have the Project files and the Assets, I'd do the work there and just turn my back on the Exported files. If you "logo" is either static, or could be "animated" in Premiere, I'd just create it in Phothshop with a transparent background and Import the Layer that you need.
I only hope that your client has the budget. Also, get "hazard pay," since this will be a tedious process, and you'll likely want a holiday, when done.
H264 can be used in Flash (CS 3.02) as video source and a logo can be overlaid without reprocessing but the combination is going to be limited to playback in a .swf player in a browser with the latest plug-in..
Just wanted to post an update.
I had success with MPEG Streamclip. It allows you to add a text watermark... and I can batch process! Having a logo watermark would be ideal, but "© CompanyName" will suffice since it will take a fraction of the time compared to doing each file individually in PremierePro.
I have high quality PhotoJPEG QT versions of each video (that I used earlier to convert to H264). I can batch process these with MPEG Streamclip. I can also try CleanerXL for batch processing, but I don't think it's export quality is that great, but it's worth another look.
Thanks for the earlier suggestions. Let me know if there are any others.