not seeing the situation makes it hard.
you can use a flexi. but not being a fan of them they look untidy and don't last like copper.
depending on the standard that you want your bathroom to look, and if you are going to tile the walls i would dig the pipe out of the wall and alter then make good for tiling.
if painting the wall you may be left with marks where you've refilled the pipe channel.
but personally i would relocate the pipe and run in chrome pipe finishs the job off better, it's the little bits that can make or break the job.
hi-spec plumbing
August 2007