Nah, he kept the Starfire PUP in there all the time. His son has the bass now, and Fender made a Custom Chop replica of it years ago. Berry just moved the neck PUP to back by the bridge when he put the bidg Hagstrom single-coil (that's who supplied those Guild PUPs) in the bass. Under his right hand you can see both Jazz PUPs.
There may be two of the modified Jazzes too. The one Fender copied is a natural finish, but it looks like a re-fin so it may be the same bass stripped and finished in clear.
jte