FD have changed it in the past, but rarely. Like Sapyx mentioned, water worlds and Earth-like worlds got a visual make-over before Horizons - and either at that time, or sometime before it (I can't remember if they coincided or not), ELWs had their criteria tightened. Which meant that some planets which were Earth-like before were turned into water worlds. Mind you, these were still the same planets, they just got re-classified.
As far as I'm aware, two existing systems have ever had their bodies modified. One was Ceeckia [something], which was renamed to Beagle Point, and this accidentally remade the entire system. Somebody at FD must have forgotten that apparently, they use the system name in the seed for system generation. The other was when Core Sys sector [something] was renamed to Trappist-1, and had some of its bodies modified as well.
So it is possible to modify some systems, but these were only examples of one. Whether redoing millions of systems would be feasible is an open question - but would it even be necessary?
As for adding new systems, that should be entirely possible. FD have added new recently-found systems from catalogues from time to time, without any problems AFAIK. They could probably add new procedurally generated systems without (m)any problems too, although that depends on how the galaxy generation actually works. But if nothing else, they could do an extra pass after what we have already, to generate the new systems.
