The 'Charlottetown' of Liza Jane is assumed to be Charleston, South Carolina, by the Bluegrass Messengers (see links to Bluegrass Messengers, above).
It had large fires, including the fire at Fort Sumter, 1863.

Charlottetown, Prince Edward Island, had two large fires, in the 1860s and 1880s. It was an important town. (see links to Bluegrass Mesengers, above)

Charlotte NC had a mint (nearby gold mines), and was occupied by Confederate forces in 1863, but had no fires of note. It was a small town at the time.

The verse in Liza Jane is early 20th c., and may refer to no particular fire.