Here's a more recent summary of what is in Philp Duffy's National Archives 42Va compiled service record, which is the only record I have found of his service in the 42nd Va.

DUFFY, PHILIP: Pvt., Co. F. Enl. by 6/64 when, as he later claimed, he deserted unit at Cold Harbor. Captured near Turkey-pen 3/28/65 when, after stating his willingness to take oath, was sent from Pungoteague, Accomack County, to Provost Marshal Eastern Shore, Va., at Norfolk. There on 4/1/65 was among a group of men "claiming to be deserters from the rebel army" who the provost marshal turned over to federal authorities. No further record.

In short, the only evidence that Philip Duffy served in the 42Va is the story he told his Union captors after he was captured in March 1865 near Turkey Pen. I don't know that it would be to his benefit to lie about his service in the 42nd, but I have not been able to verify it by other means and do not have an explanation for why he ended up in Turkey Pen. I thought perhaps he might have served in the 42nd Va. Cavalry Bn., later part of the 24th Va. Cav., but he is not listed in that unit's roster. Didn't know where Turkey Pen was until now, but if it is near Craddockville, in far eastern Va on the Delmarva Peninsula, then Philip Duffy did travel a long way from the Cold Harbor/Richmond area. But that journey would have been less daunting if he sailed across the Chesapeake Bay from the Virginia eastern shore.