If we cannot find the answer to the research question we've posed, why let that stop our progress? Let's try reframing the question.
In the case of Anna Flanagan and her disappearing husband, Stephen Malloy, we've been unable to find him in the townland—or even the civil parish—where he mailed his last message to her. Granted, searching for the surname Malloy can be challenging; in the few documents where I've been able to locate his surname, it has been spelled in just as many different ways.
Indeed, searching for Stephen—or anyone with his surname—could be a challenge. As we've noticed from researching others from this location and time period, spelling could be a flexible skill. That surname could be rendered Malloy, as we've seen in some records once Anna settled in Chicago, or it could have been recorded as Moley, as the letter had been addressed to Stephen's wife. In fact, besides the most common spelling of Molloy—derived from the Irish phrase meaning "proud chieftain"—and Malloy, the name had been anglicized to several other formats, as far ranging as Mulloy is from Miley.
With the number of possible spelling permutations, in order to conduct a reasonable—to say nothing of exhaustive—search would test the patience of even a saint as Irish as Saint Patrick. While I continue to pursue such a quest in the background—genealogy and sausage-making and all—we can attempt to answer our research question by reframing it.
We need to remember that there was a third party in the matter of this letter from a disappearing husband to his wife: Catherine, daughter of Stephen and Anna. Born in Ireland sometime before the date of Stephen's 1849 letter, surely Catherine would have left a paper trail of her own. As the child of Catholic parents, if nothing else, she would have been baptised—possibly even in the parish of Ballyagran of which her uncle William Flanagan was so proud. She, too, would have made the journey across the Atlantic at some point; after all, she ended up in Chicago before the 1860 census.
Thus, if we are stuck with the question of Stephen Malloy's origin in Ireland, perhaps we can momentarily sidestep him to pinpoint where the family lived before 1849 by searching not for Stephen or his wife Anna, but for records concerning their young daughter Catherine.