Hi Max,
What offset are you calculating, is it system or ADC? And how are you making use of the data as a part of your measurement?
You really shouldn't be seeing system offset unless you have filter mismatch with your analog filtering. For the ADC it is best to use the SELFOCAL. This will take multiple measurements and average them. Noise with any measurement needs to be minimized as it will affect the result. Reissuing the SELFOCAL from time to time is a simple way to keep any offset drift affect of the ADC to a minimum.
The overall benefit of the SELFOCAL is that it is a background process that updates the values of the OFC registers. The output code is automatically adjusted based on the OFC registers. You should always issue the SELFOCAL at startup as a very minimum.
Best regards,
Bob B