The gearbox housing was cleaned with a special cleaning device, so all oil and dirt were off. The gearbox was removed. The gear shafts made a grinding noise when turning, it turned out that this came from the bearings. Since all ball bearings had these running noises, I ordered also equal a set of new ball bearings with polyamide cage for better quiet running as they are used in my RS125.
Drilling out damaged screw 
Gearbox Oil Pump 
It was interesting to find out that the RS250 has 2 oil pumps, one oil pump for fresh oil delivery to the cylinders (2-stroke oil) and a pump in the gearbox that pumps the gear oil onto the bearings. Unfortunately, it seems that the oil pump is driven by a gear on the gearbox output shaft, which is driven by the gearbox input shaft – even in neutral.But this means: If the clutch is pulled while the vehicle is stationary, the RS is no longer supplied with fresh oil.
I was already warned in the Apriliaforum.de about the screws of the gearbox. All but one of them were opened by raw force and good screwdrivers. I had to drill out the last one, but luckily this was done from the back (see picture below left) and it was possible to fix the part directly on the drill table with a screw and a screw clamp thanks to the flat surfaces. I recut all threads of this gear part to remove the remains of the screw lock. The countersunk screws with cross will certainly not be reused, I will get some TORX head screws for the gearbox, because you can open them without damaging tools or screws.