I hoist a flag that means "three-masted ship". You see the flag and write down "three-masted ship". Because i can convey the idea of a three-masted ship with a flag and you can write down the idea of a three-masted ship with ink, the idea of a three-masted ship is not physical. The flag and the marks in ink on paper are physical representations of something, an idea, that is not itself physical. This is the argument, yes?
If I draw a picture of my house, the picture is a physical representation of a physical object. If I draw another picture of my house, I have another physical representation of the same physical object. Having two distinct physical representations of something does not entail that what is represented is not itself physical, not even if those representations are dissimilar in some way, if, say, I use pencil for one drawing and charcoal for the other, of if one is a drawing and the other a photograph.
So, in your argument, it is not that there are multiple representations in different media that leads to the conclusion that what is represented is not physical; it is that what is represented is said to be an idea, not a particular three-masted ship, but a generic object, any member of the class "three-masted ships".
Thus in your scenario I am not conveying a single piece of information, but at least two: by hoisting a flag at all, any flag, I indicate that some object exists; by hoisting the particular flag I do, I indicate that the object is a member of a particular class. More particularly, flags indicate ships, and even more particularly, ships that I can see. I am not to raise a flag hypothetically.
Is the raising of a flag a physical representation of a ship the way a drawing I might make would be a physical representation of my house? Well, it's not a picture of the ship. If anything, it seems more natural to take it as a representation of my state of seeing-a-ship. Is it a picture of that? Hmm. It would seem not. Is it a representation at all? Well, it's certainly a symbol: my hoisting a flag indicates that I am in such a state. I don't think that's exactly what we usually mean by "representation", but I suppose we could make that work by defining our terms suitably.
What hoisting a flag has in common with hoisting a particular flag is that it too is generic: I do not have a flag for each particular ship I might see, and hoisting a flag does not indicate that I am seeing some particular ship, but that I am seeing some ship or other, again, a generic member of the class "ships". Similarly, I am in the state of seeing a particular ship, but what I indicate is that my state is a member of this class, seeing some member of the class "ships".
Thus my flag hoisting conveys two claims of class membership: one about my state, and one about the object that brought about that state. Agreed?