Hydrogens are a bit of a problem, since many programs do not conform to the PDB convention which says that the first two characters of atom names are reserved for the chemical symbol, which is to be right-justified (" CA " is carbon, "CA++" is calcium). When O reads an Asn HD21 (X-PLOR), it will not recognise "HD" as a chemical symbol, it right-shifts the name so that the symbol is " H", and looses the "1" at the end. The result is that the atom name changes from "HD21" to " HD2". The same happens with Arg "HH**" (X-PLOR), but not with Gln "HE**", since O now thinks that these are HELIUM atoms ...
Possible solutions:
When the mmCIF is a fact of life, the problem will go away.
From 940323, MOLEMAN contains a command (O2XH) to restore the proper hydrogen names after they have been mutilated by O.