The issue here is that nGen File stored its file data differently than the File fieldtype (and Matrix’s File celltype counterpart). nGen just stored the filename, whereas the File field/celltypes store it in the "{filedir_XX}filename.ext" format.

I just came across this post by Rob Sanchez which outlines a SQL query you can run to update your field data, and this response that rejiggers the query for Matrix data.

Hope this helps others down the road.