Wouldn't it be easier to recompile the broken models through a different exporter, like the Truespace one?
I thought the same thing, but I'd forgotten about smoothing. One of the biggest advantages of the pof exporter is how it preserves smoothgroups beautifully - far better than PCS2 can, and moreover PCS2 can't export those smoothgroups from the POFs in the first place.
So, if I were to re-convert say, the Hecate I would have to manually try and recreate the smoothgroups one by one using TS's retarded handling of the smoothing system. This would take forever and look really crappy.

It's kinda a trade off one way or another with all the conversion methods.
- The POF exporter does beautiful smoothgroups, converts directly to POF meaning it bypasses TS, but it often has major stability issues with the POFs it produces.
- Using TS as a launching platform usually produces stable POFs, but means you have to try and use the thing in some way - which is a horrible thing.
- Using 3d exploration as a launching platform can sometimes bypass TS, but usually mucks up more things than that solves.
- Using Blender as a launching platform with Waters modified COB export script usually works very well, but you won't have much control over smoothgroups at all since Blender barely supports them anyway.