Mike,
Since pickups have no physical contact with the strings, they cannot have any effect on intonation. Intonation is strictly a function of string length, tension (tuning), and location of harmonic notes in relation to fretted notes. The only direct adjustment is the forward or backward movement of the bridge saddle and neck movement.
I suspect that since you did not make any further adjustment of the bridge saddles, there must have been slight neck movement due to environmental conditions (Temperature, Humidity), or even how the Bass has been sitting (on its back or standing upright) in its case.
Changing the pickup height will affect how well the magnetic field captures the string vibration. It may sound weaker or thinner, but it will not have any effect on intonation.
You may notice slight changes in the intonation from time to time but that's normal.
I think that fiddling with the pickup height may introduce other changes that affect the sound that you may not ultimately like.