This is a well-known pH problem that we call Diffusion Potential. If the sensor junction is partially plugged the electrical contact between electrolyte and process is not good. This results in a high diffusion potential and an error in the measurement. The chemical composition of the pH buffers is different from the process solution. So when the junction is partially plugged it creates a diffusion potential that adds to the potential from the pH buffers, and you calibrate for this total potential. When you return the senors to the process the diffusion potential changes causing a shift in the pH value displayed by the Transmitter.
An easy check is to look at the diagnostic information on the pH analyser: Is the Asymmetry Potential high or the Slope low? If either occurs then most likely you have this problem. You can try cleaning the sensor to reduce the diffusion potential.
Another cause can be the infamous ground loop current. This can occur when you use pH sensors without a liquid earth connection.