I remember hearing that many of the records were destroyed but couldn't remember if it was fire or human stupidity. Most of the reference material I have seen on Florida and/or Florida events from way back are from private collections or collections at different universities. I know the speaker from the Fl Archives told us what they did have seemed inadequate for the span of years and events that involved the state. It's sort of like the crazy system with birth and death certificates. I can't recall the exact year but if you want one from before 1913, you have to get it from Jacksonville. After the 'cut off' year, they're in Tallahassee but can be accessed at local health departments. I was lucky that most of my direct CW Grandfathers lived until after the cut off date so I was able to get their death certificates here from the county health department. I'm finding them very interesting in sorting out certain health problems that can be genetic.
Though Jeb Bush was unable to get the entire archive moved to the University of South Florida, I've heard some material was released to their care. It's like 400 years worth of history has just been scattered and no one knowns what part is located where.