Dan - the last time I spoke with the relevant bod at the CAA he assured me that your HK mob had now been put right about this.
That was a couple of years ago now, so I don't know what the current state of play is.
The JAR-FCL ATPL(A) is lawful within JAA-land airlines whether or not it was obtained with theory credits for military service. It is licence conversion which may prove difficult; if you wish to fly for non-EU airlines then check first!