Are you in a NEFEC county? their virtual school options are linked with FLVS.
My DD9 is currently in 7th grade, however is taking algebra 1 and 8th grade science with "my district" (aka FLVS). 2 years ago she was in 3rd grade and took that FCAT, last year she was partially homeschooled and partially schooled as a 6th grader. The end of the year she took the 6th grade FCAT. The system doesn't care that she doesn't have 4th or 5th grade score, it is not that smart. Seriously, that would require that when she sat down to take the test her name (which is not so unique that there wouldn't be another one in the state) would have to have been linked to her record and shown a discrepancy, and it is not that sophisticated, especially since elementary tests aren't on the computer.
This year, she will take the 7th grade reading FCAT, the 8th grade science FCAT and the algebra 1 EOC.
Yes, it took a lot to get this sorted out, but when it comes right down to it, there are laws that say acceleration is legal and that appropriate education is also required. As far as the FCAT scores not being on a child's record later, the system will not question it. The person DH talked to at the DOE said that it won't be until all of the middle school curriculum gets converted to the common core standards that there will even be an actual "course requirement" for middle schools, elementary will not have that level of requirements.
Good luck.