Do these files have any sort of meta data associated with them? It would be very useful because a one time import script could be created that adds the necessary WP references and data. Even if not, it may be worth creating the data and writing the import script. It would possibly be easier than manually creating the references, and certainly less error prone.

After a fresh WP install is made, upload a video file to WP so a model exists for what the import script needs to replicate. Every media file in WP is associated with an attachment post type. These attachments are typically children of blog posts (post post type), but it is not a requirement. Requests and searches in WP are typically for blog posts, not attachments, but almost any scenario can be accommodated with some custom coding. The attachment will also have various data related to the file in the post meta table. Your import script would need to create this data as well. Depending on the PHP function used to add attachment posts, this might be done automatically. Lower level functions will require the script to do this. Any additional meta data could go in the post meta as well.

The video files can work in their current location, but for consistency, it’d be a good idea to move them to /wp-content/uploads/. In ‘nix O/S, you don’t actually want to ‘move’ them, instead use rename to alter the path. Rename will run much faster since the files remain where they physically are on discs, only the path reference in the indexes is changed.