Deep breaths.
Keep in mind Admissions people can see everything in a candidate’s “digital bin.” The checklist in the candidate-facing portal is simply a convenient status posting, and apparently there is an issue with that particular element updating.
If your son is worried about any particular piece and whether Admissions actually has it, he can come up in the chat widget accessible on the Admissions page, and ask. He should have his candidate number handy. Live chat tends to be midday Eastern time.
USNA teams have begun working through applications and determining which applications they want to initiate DoDMERB for. Some don’t start DoDMERB until well into the cycle, and DoDMERB processes can be active through late spring. It does not have to be done by the application submission deadline, as it is not an element under the candidate’s control, though the candidate shouldn’t dilly-dally once directed to do it.
It’s not an impasse. It’s the normal pattern of stop-start, wait, repeat.