The description of transmutation spells is
Transmutation spells change the properties of some creature, thing, or condition.
So if a transmutation spell was cast after an alter self, and then the alter self was dismissed. Is the transmutation spell still active.
In this particular case, I am look at a transmutation spell that affects the eye sight. (The spell is called dragon sight). The spell Alter Self does not affect eye sight, so I am assuming that the transmutation spell is still in affect.
However, what happens if after an alter self, enlarge person was cast. And then the alter self spell was dismissed. What happens to enlarge person?