If the 1000v diode can handle the current, then yes. It I'd commonly done.
Back when some of the traditional diodes first came out in the 60s and 70s, they really struggled to make the higher voltages, do it suited them to sell lower voltage version at a much lower price. If you look at the data sheets for the 1n400X range, they all have the same forward voltage drop, so that means they were always trying to make the 1000V 1N4007, but it worked maybe 1% of the time. All the ones that didn't make the grade became 50v to 800v diodes. Now they can probably make 1N4007s with their eyes shut.
But just double check the spec for the forward voltage drop at the current you are using. If the 50v diode is less, it will run cooler.
Richard