Of course files can be deployed to store the information you need. What worries me though, which depends on how your game works, is that all your bases will need to continue doing what you set them to do, regardless of whether your are watching or not. This means that, for each bases update you will need to read all the information from the hard disk. Bear in mind that in programming, wherever you have I/O operations, they are the bottleneck of your game's performance.
Of course, I have never worked on such a large scale project and I am not sure how the multi-base functionality is implemented in AAA games. Probably there are multiple threads, one for each base that constantly update their state.