If a sythesist is poisoned while merged with it's eidolon, does the poison effect both. For example, would Con lost effect both the character's hit points and the temporary hit points gained from the eidlon?
Generally, kinda. Specifically, maybe.
When the synthesist is merged, it's really more one creature than two. It has one set of stats. If you poisoned the fusion and then banished the eidolon, the summoner would stay poisoned.
However, the temporary hit point deal is tricky. You're using the eidolon's ability scores instead of your own. This normally means you double dip for bonus HP to your personal HP and the temporary from the eidolon.
However, if the eidolon's ability scores were reduced, then both your personal HP and the temporary HP should be reduced.
I'd say yes.