Please upload the updated version, maybe transferring all storage to some storage in the central section of the map... maybe let the player choose which faction has them so relationships don't *** you over.
A solution to the colonies not existing could be to simply giving the player a choice to pick which planets are given all the infrastructure of old ones, or are simply replaced by the colonies? A more immediate alternative would be to simply give the player their cost in cash, but that doesn't account for the time they take to be built again.