Assuming you are talking about an M Series BSA it is possible...
The crank case 'register' on these engines was machined in the same operation as the main bearing housings...
So, if the register is a good fit (the lip on one half of the case into the recess in the other half)then the main bearings will be in alignment...
You will need to check that the cylinder mounting face is level and also the magdynamo mounting platform when the two halves are bolted together...
If not the crank cases should me mounted on a milling machine, the lower half clocked true and the faces skimmed to level them up, removing the minimum amount of material...
Before machining ensure that when the two halves are bolted together the two faces mentioned above are as true as possible in relation to each other...
Finally you will have non matching numbers for the two crankcase halves...
If you want them to match they will have to be removed and re stamped...
In case you have the magdyno platform machined, check the drive gear afterwards, when you rebuild the engine.
It should move "free" when mounted and tightened, to prevent tension.
That is a good point, though checking the mesh of the magdyno gears should ALWAYS be checked after changing the mag or crankcases or even after removal and refitting of a mag to the same engine....
An over tight mesh of the gears loads up the magneto drive end bearing leading to premature failure and the gears will whine audibly when running.....
Too slack a mesh will rattle when running...
Also check frequently, particularly on a recently rebuilt machine, that the magdynamo strap bolt has not loosened...Ian