AFAIK (private person's knowledge) it boils down to this: 3DR own the rights to DN3D (and the other pre DNF games) and they can do with these games basically what they want. But, there must not be any new games 3DR/Apogee Ltd. (and also Apogee LLC) don't have the rights for.
I recall somebody asking for some new version of Duke2 (can't exactly remember what it was, but it would be something like an enhanced remake) and Fred answered that this suggestion would basically be a new game which is prohibited.
And remember how it all began (publically available to read on GBX' forums if you really want to visit that place). Fred releasd some screens and asked Scott Miller for allowance to make reloaded who pointed him to GBX, so this alone tells us that Reloaded would be a new game. Imagine it just like that new Shadow Warrior game or even the ROTT remake.
EDIT:
And I think EDuke was never in danger to be put on hold by GBX. But now even less than before. GBX and the mods became really defensive and quite after the A:CM debacle (they lost a lot of reputation when you look at gaming sites nowadays. and there is also the lawsuit, etc...). You can now basically insult them and the mods on their own forum with the harshest words now and "call them complete idiots who should hide under a rock and never come back" without even getting one single warning point. How do I know ... well ... I heard somebody said that and got away with it.