Flinders could have done with this knowledge. Despite being on a scientific expedition and in possession of a passport issued by the French government allowing him free passage (Baudin had one as well issued by the English), he may have thought to change his mind and not gone to Isle de France. He was arrested there and interned for seven years.
Britain and France were at war on and off all the time and it was very difficult for people in the South Seas to keep track of it all.
The log entries for when the Rolla was in the road and in harbour are written on seperate sheets and tipped into the logbook, whence it starts again once having left the port. Not sure of course, but I think this is because the ship's papers - including the log - would have been in the hands of the Harbour authorities to make sure their was no shenanigans.
I've copied out the entry here:
Monday 5 December
Moderate breeze with cloudy weather People variously employ'd
seamen as necessary Passed down the River three Americans
hailed one of them named the New York bound to
New York who informed us it was believed there was
war between Great Brittain and France Wind ESE