If you group the star charts in 4x4 groups, that's 125 files for 2000 star systems, and each file is 128K, occupying 16 segments. You could have a rectangular master map and compute which cluster you need when leaving a system that is on the edge of a cluster.
And with only 125 files, each "cluster" map can be indexed with a single byte, so you can have a linked master map and aren't limited to a rectangular master map if you don't want to be.
BruceMcF's post in "Lots" of data files was marked as the answer