When a Synthesist summoner summons their Eidolon, they fuse with it becoming one. As I have checked with another question, an Eidolon can be affected by control summoned creature spell, and the original caster can still potentially dismiss their summons.
However its a bit different in this case as the two are one.
The information that deals most with this is
While fused, the synthesist loses the benefits of his armor. He counts as both his original type and as an outsider for any effect related to type, whichever is worse for the synthesist. Spells such as banishment or dismissal work normally on the eidolon, but the synthesist is unaffected. Neither the synthesist nor his eidolon can be targeted separately, as they are fused into one creature. The synthesist and eidolon cannot take separate actions. While fused with his eidolon, the synthesist can use all of his own abilities and gear, except for his armor. In all other cases, this ability functions as the summoner’s normal eidolon ability (for example, the synthesist cannot use his summon monster ability while the eidolon is present).
So anything that could target the Eidolon before, can still do so, but as the Eidolon is basically brain dead and just being moved by the summoner would it matter if the Eidolon is controlled or would the caster manage to gain control of the summoner and Eidolon with the casting of control summoned creature?