Why is the military title of Colonel pronounced as "kernel"? Is there an historic reason for this?

The word colonel comes into English originally from the French form coronel, so it was always pronounced with an "r." The word was later respelled to bring it into "agreement" with the more remote source in Latin, in which the "r" was an "l."

Something much like this happened to the word debt, too. This came into English from French dette, and never did have a "b" in it. The "b" was introduced by scholarly types who knew the Latin source was akin to our later borrowing directly from Latin, viz. debit.