Hi Jen,
As long as the diagnosis pointer indicates F25.0 as the primary diagnosis, there shouldn't be an issue. As you said, it is redundant, but shouldn't cause any problems. The only thing I can foresee is that by using both ICD-10 codes, it can look as though the MDM is being artificially inflated. I would suggest maybe using just F25.0 and manually adding a specifier to indicate the patient's current or most recent episode (manic or depressed). Prior to DSM-5, schizoaffective was actually a specified type of bipolar disorder, so the diagnosis would have been Bipolar Disorder, schizoaffective type. I don't think either version does a very good job of summing up the nature or variations associated with the diagnosis. Alternately, the F31.9 could have been used to indicate that the patient has other mood fluctuations that might not be associated with their schizoaffective disorder (i.e., SAD, shift-work disorder, etc.). It's a reach, but I've seen it done. It may help to go back and review the documentation to see if you can track down which diagnosis came first and/or if some justification can be found for the additional diagnosis.
Good luck!
Ginny