No, that is not the difference. Both ask whether the listener has visited Florida in the past; there is no reference to present circumstances. 'Been to' is an idiomatic form of 'gone to', while 'been in' is the normal locative meaning of 'be'.
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Nina_NiaCould you tell me if there is any difference between;I use them (slightly) differently; but many speakers use them interchangeably. There are two distinctions for me
Have you ever been to Florida? and
Have you ever been in Florida?