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
Zoning trumps building department. However, if the construction of the the 3rd unit was not applied for, inspected and reported, it may be in violation of the building department rules/regs, where-by-as the building permits were not applied for an approved.
Most assuredly get your attorney involved and take John Potter's advise and check your water bill. This may come in handy for your litigation, if it gets that far.
If that doesn't get it resolved, it is time to call your attorney. In the meantime, go downtown to the building department and find out how you have two very different opinions.
Make sure you get the names of everyone you speak with who gives you any information so you can reference them in future conversations.