Agitate in order to mix or loosen, as in This cough medicine needs to be thoroughly shaken up, or Please shake up these pillows.
Upset greatly, as in Even though no one was hurt, he was greatly shaken up by the accident. This usage alludes to being agitated like a liquid being shaken. Also see all shook up. [Late 1800s]
Subject to drastic rearrangement or reorganization, as in New management was bent on shaking up each division.