The thing is, the community would endure, it would effect Mods only visually for the main part.
What I think we would see in that situation is a reduction in the amount of Freespace Universe mods appearing, but possibly an increase in the use of the SCP as an over-arching engine for First-Person Shooter space games because of it, people will have to think of other universes to set their stories in.
The biggest loss would be all the hours and effort put in by the modellers and artists who worked on the projects like the Freespace Conversion and the FSU, but I think they are all aware of the risks of their undertaking.
Whilst I hope it doesn't happen, if it did, it would just mean a new direction, one that could give as much as it takes away.