Technically the remastered versions (which is not really a correct term since effects wise it's reimagined rather than remastered?)
They were remastered. All the live-action footage and audio was digitally restored to HD quality from the original film and audio masters. That was the primary purpose of the exercise, to make an HD-quality video release of TOS that looked and sounded far better than previous video releases. But since they didn't have access to the original FX film elements, they weren't able to remaster the FX shots to HD quality and had to replace them with CGI instead. So everything was remastered except the FX shots, which are just a few minutes out of each episode, a very small part of the whole.