I have never seen this before
I have worked with a lot of different EMRs, including eClinicalworks, but I have never seen 2 exam sections like you are describing. From a coding perspective the 2 terms, Exam and Physical Exam, are defining the same thing. When we say "exam" that is essentially the abbreviated version of "physical exam".
This sounds like a set up quirk or issue with this particular system. Not all EMRs are the same, even if they are from the same place. With most systems you get what you pay for and they have all kinds of add-ons and upgrades out there which will vary the options seen within each individual build.
The only rationale I can think of for having 2 separate exams would be if they have them set up to drive a leveling tool based on either 95 or 97 guidelines.
In that case there should one be 1 completed though, not both.
Sorry not much help,
Laura, CPC, CPMA, CPC-I, CANPC, CEMC