I’m using Magura rim brakes on my 26". Problem is that where the rim joins there is a minute step on one side of the rim, and when lacing the wheel I didn’t notice this. So what I have is an ‘up’ step when the join goes past the brake pad, which catches, rather than a ‘down’ step, that I suspect would be fine. The rim is a 10+ year old black one from a Nimbus muni of that era, 45mm width or thereabouts. Not machined for rim brakes, but a flat surface, and the original frame it was built for also had Magura mounts.
Can this step be fixed somehow safely? It’s a fraction of a millimetre. Eg I wondered about carefully sanding it flat.
I know I could flip the wheel so it spins the opposite way, but it’s laced to a Schlumpf hub, meaning it would change the side of the high and low buttons (and the orientation of the hub logos 
).
Close up view:
You can sand it flat, removing the amount of material you need to stop it from catching will not affect the rim’s strength. Also, you can file a chamfer on your brake pads to reduce the ‘‘catching’’ effect of it.
Thanks @jaco_flans, much appreciated - I love how in this forum we less experienced riders can get advice straight from the sport’s top players!
What grade of paper would be needed, and would I need to sand with a flat surface (eg using a block), or would just rubbing with finger pressure be OK?
Sometimes it helps to turn the rim 180 degrees (don’t forget to remount the cranks) when the gap in the rim is higher on one side. There are problems when the brake pad hits the higher edge, but not when it goes down. But it only works if the edge left / right is identical. (I hope you understand what I mean was translated with translator).
Definitely use a block, otherwise you’ll sand about as much off from the sides of the bump as from the bump itself. I would use 400 grit to take down the bump and then finish with 800 to get it to match the finish on the rest of the rim. I’ve never actually done this but I’ve sanded lots of metals so those numbers should be close and get you a decent finish.
I would personnaly get a very fine half round file and give it one or 2 shots before sanding, but I’ve grinded rims on my Trials bike with an angle grinder before 
Also, I’m really confident with tools.
I would use a block, and try to keep it flat as much as possible. To make sure you do it right, you can skip the file part and just sand away with the block!