"West Virginia in 1860 was part of Virginia." " West Virginia officially became a state in 1863." Ref. Map Guide to the U.S. Federal Censuses, 1790-1920 by William Thorndale and William Dollarhide. Pages 374 and 375.
Since the son of James Fahey and Bridget Lynch, Patrick H. Fahey, was born 5 Jul 1862, he would have been born in Virginia one year prior to WV becoming a state. The Civil War began in 1861 and ended in 1865.
What was reason for the red flag?