Certainly sounds like they tried to hide his gear id.
Maybe got spooked by another boat coming close by?

I would make sure he has melted his ID into the floats as well that way they cant be painted over.

 Yeah you gotta melt or carve your id deep into the float. Another trick they do is just cut your float off and put there's on. So you gotta engrave deep your id in the pot. Still no  guarantee. Painful eh??

 There are just too many dickheads in the world of fishing, most of us are descent people who respect each other as we share a common passion but then there are those few who think they can do what ever they like, in the last 6 years all my pots have gone missing in the first week or two but still i try every year hoping that the faith i lay in my fellow fishers will pay off.

 Last couple of seasons Ive pulled my pots out before school holidays started. Havent had any trouble outside of holiday time. Had heaps of problems with pot tampering previously - during holiday times. As Brooky says, most fishers are like minded but the more boats on the water - the more chance of an arsehole paying you a visit.  

Sounds a bit suspect to me.

Who is going to take a can of paint out with him in a boat and try to get paint to stick on a wet and probably slimy float, doesn't happen in my book.

 Yes, must have swaped the float - not painted  it. Pro octopus floats in Mandurah are blue. Maybe someone was just playing silly buggers & thought it funny to mess with the floats. 

 I'm thinking it could've been run over but not chopped by another boat with anti fouling on the hull. I used to work on a boat with a blue antifouled hull and any floats that got run over ended up blue.