Check the following reply that I posted on another thread:
I go through a detailed procedure for upgrading from V4 to V5. I think the problem you are encountering is due to the fact that once a footprint is placed in a board file, the libraries are ignored. The placed footprint is now embedded in the board file. This allows lots of latitude, like making subtle changes to the footprint in the board w/o having to change your libraries. But, that means that if you update the library the footprint in the board won’t see the library changes. Because the 3D object found by a pointer parameter in the footprint, updating all your libraries to V5 won’t magically point the footprints in your existing board to the new 3D libraries.
I think in my procedure steps 12.2 and 12.6 should help you get the 3D object pointer parameters pointing to the modern V5 libraries. As I warn in 12.6 you may need to find some new (or extract old from a backup of the V4 3D libraries) models.
You may want to read through the full procedure to make sure you haven’t missed a step along the way.