I presume this voids the warranty but is it possible to use the existing cooler on the R9 295X2 as part of a custom loop as it looks like the tubing is just attached to the radiator with barbed fittings, if I removed one of them and attached it to a custom loop would there be any issues?
It would probably void the warranty. If you're going to do this, I'd take the stock cooler off completely and get a proper water block for it. That way, you can't ruin the cooler if it had to go back for a repair for whatever reason. I am aware that removing the cooler can void your warranty, but it is far less likely to be rejected than a pulled apart stock cooler.
the tubing and barbs on the AIO coolers are of an odd size. When i modded my antec 620 (another asetek unit) i had to leave a small amount of the normal tubing over the bars and fit 13/10 tubing over the top of that. link's in sig if you want a look.