There are two Thomas Flynns of the same age (31, both born in NC) in this Census. One listed here with a family, the other listed with Thomas' brother William. Either there are two and for some reason, Thomas was counted twice.
1840 Census. Greene Co IN
The Flinn book states that Thomas married "Permelia"; the online marriage record says "Permetia". There's no other marriage record for Thomas. A deed of 18 Nov 1852, gives her name as Sidney Amelia Flinn. The 1850 Census has Sydney A. Either she married as Amelia and the name was misread or Thomas married twice. I believe it's the same lady.
1860 Census. Richland Twp, Greene Co IN Hh 1009
Thomas's brother Josiah Jr. is living in the next residence.
Thomas FLYNN and Sidney Amelia MCDONALD were married on 24 December 1838 in Greene County, Indiana.59,118 Sidney Amelia MCDONALD, daughter of Joseph MCDONALD and Permilia [MCDONALD], was born in 1815 in Ohio.59
Thomas FLYNN and Sidney Amelia MCDONALD had the following children: