The first printing of Close Encounters had replacements for the base game counters. AFAIK there has not been a second printing of CE yet, so if you have the expansion you will have all the counters there are.
Do I have enough counters for various base game and first expansion scenarios with just those that come with Space Empires: Close Encounters
Sometimes I read that the counters in CE replace those in the base game entirely, so that would seem to mean that I have enough without having any counters from the base game.
Just looking for confirmation or revision of this judgment!
I've been playing solo doomsday so I haven't really stretched the counters to the limit. I only have CE and the base game map.