You are the first line of defense because it is the status of your "Serious Health Condition" that is at risk here. Follow the rules, ie., if an FMLA absence is foreseen, advise management no later than 30 days prior to the actual onset of the absence. If an FMLA absence is not foreseen, advise management as soon as practicable. Now, the term "practicable" can mean many different things to different people, however, circumstances will dictate what is, or isn't, practicable for any given absence. How those circumstances are interpreted is an entirely different matter.
Verify that the certification form is complete. Do not let your doctor expound on your health condition beyond what the law requires. Utilize your Union's FMLA certification form (if available). It is simpler and less frustrating to complete.
If you have a "chronic serious health condition" insure that the "frequency" question is answered as honestly as possible based on your medical history. To wit, if you were absent nine days on three separate occasions on your worst month, and zero days on your best month, your doctor should annotate "zero to three days per incident", and "zero to three incidents per month". To have your doctor annotate "zero to thirty days per month" just because somebody wants it that way makes a mockery of the law.
If you have more than one chronic serious health condition then apply that reasoning to each condition. If you exceed the stated frequency, then a recertification of that particular condition would probably, but not necessarily, be required. That would depend on your FMLA Coordinator, and how the law is applied by that person. It was the intent of Congress that the FMLA be administered in good faith and cooperation. Whether that intent can be achieved at any given installation is questionable.