I'm sure they wouldn't bother, but seeing as the model work was also shot originally on film, the option exists to re-composite certain VFX shots as well
I'm sure for consistency of TNG-Remastered for 7 seasons they would do all exterior ship visual effects
with CGI Ent-D.
Also it would be less of a hassle to find visual effects work that didn't include actors.
I was going to suggest this too, if they are going to do SOME FX, whether or not the 35mm negatives exists, they will want to make it coherent...the same way they changed the music and titles for all episodes of the TOS-R remastering.
The June 2010 link has some useful technical info on how STNG can be remastered.