When a Synthesist fuses with his/her eidolon and they have superior ability scores (such as Con), is the intent to reduce those scores to the Base for the eidolon (in this case, lowering the summoner's overal HP and reducing the Fort save bonus)?
The intent is that you are the creamy chocolate center of a unholy murder machine. Your Con doesn't really matter until your Eildolon shell cracks. So while you're fused together, your effective Con is the Eidolon's, be it higher or lower than your Summoner's.