If you truly own the land, then the dock is yours. You mention a document from TFI. If you are referring to the Florida Internal Improvement Trust than a Deed from them would certainly give you rights to the submerged lands of that particular parcel. As to the other parcel, you would need to trace back the private ownership to make sure that it is fact private and not owned by the State of Florida. Upland or Downstream is irrelevant as to the ownership. What you are looking for is for the submerged land boundaries of the dock area to be included in the deed and a traceable exception to the rule that submerged lands belong to the State of Florida.
Title to land underwater is a "murky" issue (pun intended). Here in the Northeast, I have researched title to lands underwater that go back to pre-revolutionary war era grants from the English monarch. Depending on where the grant is located, it may involve federal, state, county or municipal riparian grants or claims.
If you have a deed conveying an ownership interest in land underwater, and Florida permits such transfers, then the hotel is bluffing. On the facts presented, there is no way to tell.
You will need a local real estate attorney to review your documents and advise you on the issue.
I am not a FL attorney, laws vary from state to state, therefore you should always consult a local attorney.
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