Has anyone ever been denied an assignment to a base overseas because of EFMP, but was subsequently cleared a couple of years later?

EFMP denials are normally based on the availability of the specialty care or considerations needed to treat or facilitate the EFMP condition. If there are no Army-sponsored facilities or accommodations available to provide the required service, the assignment can be denied. If the facilities or educational services do exist but are at capacity for that assignment area, the assignment can be denied based on capacity at that location. In the second case, it is possible that another family might PCS away creating capacity at that location, but to my knowledge, the stars would have to align within the Soldiers branch for them to be available to move at the time that the vacancy and EFMP capacity exists. In my experience, it was often difficult to get a clear answer on whether there simply was no way to facilitate a condition at all, or whether it was a capacity question. If your son was EFM in Japan the first time, then the question is whether the required service no longer exists or whether they simply have too many at this time. I'm sure that answer is helpful and not helpful. Sorry about that.
"Commanders of OCONUS travel approval authorities
These commanders will— a. Coordinate with medical and educational representatives to determine the availability of required services. b. Provide a decision to military personnel divisions and/or personnel service battalions (MPDs and/or PSBs) within 30 calendar days of receiving Family travel requests involving EFMs." - AR 608-75 Chapter 1.