When documentation indicates uncertainty in the diagnosis, it cannot be coded. In the case of the doctor documenting DX versus DX, neither can be coded. Instead, code signs and symptoms, to the highest degree of certainty for the encounter, until a definitive diagnosis is given.
(This rule is not applicable to inpatient admissions to short-term, acute, long-term care and psychiatric hospital.)
Hope this helps.
EDIT:
Looks like I was a bit late but, if you have your ICD-9 book handy, I believe all of them have the Official Guidelines printed in them. Most have the guidelines printed in the front of the book, but I hear some are printed in the back. Anyway, the rules for coding probable diagnoses is there for you. Section IV. Diagnostic Coding and Reporting Guidelines for Outpatient Services, I. "Uncertain diagnosis"