Hi - If the field is a custom field (not out of the box), then (by default) Discovery won't update it.  Soo... if you are sure Discovery/MID is updating it, then I would look for business rules or some-home-grown automation that was built to update the custom field.   ( OR, you've customized patterns (or sensors) to update the custom field - but I suspect that is not the case here. )

A guess: Perhaps when discovery runs, its performing an update on the CI and you have a business rule that is triggered (on update) that is doing something to data within the custom field.

I'd look for some custom automation that was built or not behaving the way you intended.. to track down why your custom field is getting updated when discovery runs.   

Hope this helps a bit?