Peter says something in the future episode to indicate that Niki still has super strength.

All the powers are genetic mutations, so Niki has hers regardless of who's personality she's manifesting. Controlling the power is another thing, and I'm sure at some point the writers will cover that and we'll see some super strength action and a lack of the Jessica personality.

Many of the charcters have gone through some type of learning curve on the show to gain control of their powers. Niki didn't know about her super strength for a long time and once she discovered what was going on, she didn't try to harness it because she associated it with the jessica personality. For the newer episode Niki's own personality has been completely locked away, so the whole thing is moot.