I know it says that a fused eidolon and synthesist summoner can't be targeted separately. Besides the noted spells.
With that said does that mean that single targeted spells, supernatural, magical items, and anything else that specifies a specific single target has no effect on a synthesist summoner and does nothing to them?
It means that the synthesist is treated as a single entity for the purposes of targeting. Single-targeted spells affect the synthesist-plus-eidolon as a single entity.