It is likely that you were renting out your home while you were abroad. Were you? This is a common and perfectly sensible thing to do. However, if your home was rented out, it became a rental or income-generating business property--which in most places would make it ineligible for a homestead exemption/reduction in taxes. In some places that would have also increased the tax rate from the normal homeowner occupied tax rate to one of a rental or commercial property--often two or three times the home owner occupied rate. If this is what happened, because you were renting the property, there would be little you could do about it legally: you were in possession of a rental/business property and were taxed accordingly.
It may be that you were claiming ex-pat status which more-or-less implies that you're not homesteaded in the USA anywhere. The ex-pat status is claimed by folks trying to avoid paying federal income tax on their income earned outside of the USA.
If, on the other hand, you were not claiming ex-pat on your federal taxes and your home was empty or you had family/friends staying there, at no cost to them, to keep an eye on things, and you were not claiming that your boat was your home (as many people do make these claims to reduce tax rates on their boats in some states which tax boats which are homes differently than boats which are just..boats...) then it would seem unlikely that you would lose your homestead/homeowner occupied status. Many folks are on extended vacations (over the 1st of the year) etc. Perhaps your county in Florida has a length-of-time-gone rule but that would be very difficult for them to enforce if you weren't renting your house out to other folks. They would really have no way to know for certain when you were there and when you were not there unless the home was rented.
Most government agencies do make exceptions for the military in many tax matters--considering that they are risking their lives for their country and often are under payed for the work they do, and are often moved without any say in the matter--this is a good thing that the governments try to be accommodating.
I do assume that you're also a US citizen, as it is often difficult for foreign nationals to "prove" their homestead status as they maintain more than one home and residency in more than one country. I have a friend who is Swedish but also w/US status who walks a very fine line in this matter. Her real estate is in the USA and she spends each winter here. Each summer she is in Sweden.
Please let us know if you were not renting out your house, claiming your boat as your home, or claiming ex-pat, how it would be possible for the local government to actually ascertain that this wasn't your home.