So, what did the losers flags look like before the Civil War and readmission to the Union?
OK, let’s start with the obvious one, Texas always had the flag of Texas. However…
It seems a majority of states (southern or northern) did NOT have officially-designated State Flags until after the war, and if they even bothered to fly any sort of state ensign, it would be the battle flag from some historic or currently-important military unit. The “blue bedsheet” state flags of many northern states, for example, ARE essentially the regimental flags of their Civil War-era militia.
From the Flags of the World site:
Alabama: no state flag from 1819 - 1861
http://www.crwflags.com/fotw/flags/us-al.html
Arkansas: no state flag prior to 1913
http://www.crwflags.com/fotw/flags/us-ar.html
Florida: a whole bunch of different flags (the earliest used by Anglo-American invaders trying to take the Gulf Coast away from Spain). Included among these was the “Bonnie Blue” (a single white star on a dark blue field) that was borrowed at different times by the successor states of formed along the Gulf, particularly as battle flags during the unpleasantness from 1861 - 1865.
Florida did not have an official flag until the secession, although the Mosley flag was flown at the time Florida became a state in 1845.
http://www.crwflags.com/fotw/flags/us-fl3.html
http://www.crwflags.com/fotw/flags/us-fl2.html
Georgia: no official state flag prior to 1879, although the state seal was pictured on fields of red or blue or white at different time.
http://www.crwflags.com/fotw/flags/us-ga3.html
http://www.crwflags.com/fotw/flags/us-ga2.html
Kentucky (not a successful secessionist state): basically variations of the flag in use, today, although there was never an official flag until 1963.
http://www.crwflags.com/fotw/flags/us-ky.html
Louisiana: no state flag prior to 1912, (although a “national” flag was used during the Civil War).
http://www.crwflags.com/fotw/flags/us-la.html
Maryland (not a successful secessionist state): no official flag prior to 1904. A flag is mentioned earlier, but no specific mention is made of its appearance.
http://www.crwflags.com/fotw/flags/us-md.html
Mississippi: no official flag prior to 1861. (The Bonnie Blue had been flown on occasion.) The Magnolia flag flew from 1861 to 1894.
http://www.crwflags.com/fotw/flags/us-ms.html
Missouri (not a successful secessionist sate): no official flag before 1913. Various flags carried by Confedrate regiments during the war.
http://www.crwflags.com/fotw/flags/us-mo.html
North Carolina**: no official flag prior to 1861.
http://www.crwflags.com/fotw/flags/us-nc.html
South Carolina: the crescent on a dark blue field was selected as a battle flag during the Revolutionary War. Various versions (apparently including the palmetto on some) flew between 1775 and 1861.
http://www.crwflags.com/fotw/flags/us-sc.html
Tennessee: no official flag prior to 1905.
http://www.crwflags.com/fotw/flags/us-tn.html
Texas: the “Lone Star” flag (with a debt to the Bonnie Blue) was adopted as the national flag in 1836 and has remained.
http://www.crwflags.com/fotw/flags/us-tx.html
Virginia: The Great Seal of Virginia was adopted around 1776, but no flag was identified until the seal was put on a blue field in 1861.
Virginia link:
http://www.crwflags.com/fotw/flags/us-va.html