A period of time after you sunk the neutral (i can't remember the exact value) the country considers you a renegade and attacks you on sight.If you attack other neutral ships during this status,i think the tonnage is deducted from you at the end.About the first neutral you sink...i don't think it is deducted from you as long as you are not considered a renegade.
PS:That also happenes to me a lot of times especially at the start of the war -those damn Norvegians travel close to the English and use similar ships and in a storm it's hard to identify them
