One explanation that occurred to me (without any documentation) was that it derived from the Indian term for English colonists.
Specifically, the French allied north eastern Indians called the English colonists by the same term that their French allies did, “l’anglais,” which could have devolved into “Yankees” and might explain why the name was only used for north eastern colonists.
I could well imagine that British officers and regulars stationed in America during the French Indian war would adopt this term for the colonials as a derisive one.
Again, no evidence although perhaps research any variations in spelling of “Yankees” from early writings might yield some support.
Yankee1683, a name applied disparagingly by Dutch settlers in New Amsterdam (New York) to English colonists in neighboring Connecticut. It may be from Dutch Janke, literally “Little John,” diminutive of common personal name Jan; or it may be from Jan Kes familiar form of “John Cornelius,” or perhaps an alteration of Jan Kees, dialectal variant of Jan Kaas, literally “John Cheese,” the generic nickname the Flemings used for Dutchmen.
*t is to be noted that it is common to name a droll fellow, regarded as typical of his country, after some favorite article of food, as E[nglish] Jack-pudding, G[erman] Hanswurst (“Jack Sausage”), F[rench] Jean Farine (“Jack Flour”). [Century Dictionary, 1902, entry for “macaroni”]
It originally seems to have been applied insultingly to the Dutch, especially freebooters, before they turned around and slapped it on the English. A less-likely theory is that it represents some southern New England Algonquian language mangling of English. In English a term of contempt (1750s) before its use as a general term for “native of New England” (1765); during the American Revolution it became a disparaging British word for all American native or inhabitants. Shortened form Yank in reference to “an American” first recorded 1778.
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The supposed l’anglais/Yankees alteration is one of several existing theories for the etymology of “Yankee.” It lacks contemporary support, but so do most of the others.
I have no idea whether this has any legs under it, but…
Could it be that Yankee was derived from one of the Dutch epithets above, adopted by Royalists (Primarily Virginians) as a term of derision for Roundhead sympathizers living in and around New Netherlands? 100 years thence, the usage by British soldiers and Southerners seems a likely consequence.
I know that the “nickname for Dutch-speaking Americans” is pretty well accepted, but what about the Cavalier Connection?