Inserting Controls in a logistic regression

A beginner here, so bear with me :)

I have 3 groups of patients and 1 control group. There are many independent variables to be tested. However, a couple of these variables are concerned with "onset" and "duration" of disease. Both would be ordinal variables if it wasn't for the "Controls" as controls here take the "inapplicable" code.

Does this mean i have to treat both variables as nominal creating dummy variables and all?

is there a way to maintain the order of the categories and hence the measurement level of the variables other than excluding controls from my analysis?