Yeah, my problem isn't knowing where the .flv files are. Moodle knows where they are. All I have to do is tweek the record for the link - add the missing intro text and set the type to automatic, and it works great. My problem is automating this task so that course administrators don't have to do a simple GUI edit task over and over again after the upgrade.
By the way, it's not just the video files that are stored differently under 2.0+ - all files are stored in a proprietary setup. The former moodledata directories corresponding to the course ids are all empty. It has moved to prorpietary files in the filedata directory. Now everything must be accessed through the database and/or program code. I think the developers did this in an attempt to improve overall data integrity.
: ) Chris