One theory:

To add to the collection of REASONS for the war, try this! Some think it was
a continuation of battles in Europe which had been ongoing for centuries. The
English, with their red, white and blue flag, battled the Scottish Highlanders
who had chosen a flag with blue field and white St.
Andrew's cross. The English migrated to the North and New England while the
Scots migrated to the South and the Appalachian and Blue Ridge Mountains.
Soon they
were at it again in the great Civil War.

The Deep South had trouble recruiting men to fight until leaders decided upon
a battle flag design to which the men of Scottish descent could relate. They
renewed their former flag design, with a red field where it had been blue. The
familiar cross in the middle was retained.

The Civil War was, in part, a repeat featuring British descendants in the
North, with their familiar red, white and blue flag against the Scottish
descendants in the South with their familiar flag with a cross in the middle.

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