How do I deal with data that has only limited target values?
I would try two different approaches:

interpolate the missing values on a user level.
work with the sunset of rows for which we actually have the glucose level.

Then, I would compare the test accuracy of the model built with both methods. Remember that your test set has to be composed of rows for which you have the glucose level - you cannot build it with interpolated data, that would be cheating!