Yes, they FAQed this to allow just that kind of use.
Paizo wrote:
Can I use the evil eye hex more than once on a target?
Yes. As long as you apply a different penalty with each use of the hex (AC, ability checks, attack rolls, saving throws, or skill checks), you can have multiple penalties on the same target. Applying the same hex penalty to a target just resets the duration to the most recent use of the hex.