I've been doing a little more research on this incident. In the book "From Everglades to Canyon with the Second Dragoons" (Now 'United States Cavalry' in the title.), it states that the indians did get away with some percussion caps, so they might have kept some of the rifles besides the ones that were destroyed by breaking the "locks" (I don't even think these versions had exposed hammers, and it is unknown if they were the 10 shot, smaller caliber, or the 8 shot larger caliber.)
I also read in an article by M.L. Brown, that Samuel Colt tried to sell revolving muskets (Which I never knew existed), the revolving rifles, and revolving pistols to the military, but they were not interested in the muskets, so he brought 10 cases of rifles (100), and some unknown amount of pistols, plus percussion caps (and I would assume bullet molds) to Florida in February of 1838. General Jessup was only going to buy 30 rifles, but finally bought 50 at Col. Harney's insistence. They also bought 25,000 percussion caps. There was never any indication that any pistols were purchased (I can't imagine why...I would have wanted 2!).
I think this next part might be where this story of the cased rifles falling into the river came from.....
About February 28...Colt stopped on his way back to Charelston, at Ft. Marion at St. Augustine, pressumably to demonstrate the rifles and pistols. On his way to shore, the schooner's yawl capsized and Colt lost "the precious Treasury drafts...most of his personal belongings, all of the pistols, and the fifty unsold rifles." They replaced the treasury drafts for Harneys's rifles and caps later that year. That was footnoted to be from a biography of Samuel Colt by William B. Edwards.
I would imagine that this is the source of the "lost rifle's in their cases" story....only it was the Atlantic, not the Caloosahatchee...along with Harney's statement of some being "lost at the Caloosahatchee". The story just got mixed up. That means there probably are some still off St. Augustine a ways. I don't know how far out the schooner was anchored while the smaller boat went to shore, but Samuel Colt was rescued after four hours floating in the ocean...so it must not have been too close to shore.