Your attorney should be able to help you navigate the situation.
If the Zoning Cert. says 3 units, then you are permitted to have 3 units in the property.
If the Department of buildings has a record of only 2 dwelling units, then one of two things are likely true
a. A unit was constructed without a permit, such as a attic/basement/coach house.
b. The third unit's construction predated the records at the Department.
In either case, if it's not just a paperwork error, and the attorney cannot help correct it, it may be beneficial to seek out the help of an architect. An architect who is familiar with Chicago's various city departments can help you determine feasibility of keeping the third unit and what would be involved in getting it up to spec with Chicago Building Code.
Best of Luck
312 77 BEALS