I always had an idea to reuse some (vanillia) empty systems with content from the systems being cut out. However, the catch would be ability to populate vanillia Sirius not only with bases, but also with new planets from the removed systems. Why this idea? I always found vanillia systems quite empty and it hit me even more, when I visited Gallia recently.
As for the bases themselves, they would retain their Guard status by having respectable IFF, such as in case of Zoner Guard base in Baffin.
(Don't worry LPI about your Illinois, it's just a proposal.)