As per prior post the rubber dust shield can be left on the new primary side ball bearing in an attempt to keep oil INSIDE the box (and grit out), but I'd still retain the original BSA oil seal as well, the seal towards the inner side of the box MUST be removed to allow gearbox oil to lube the bearing.
The kickstart end I've no experience of using sealed bearings there, but I can't see any advantage from having dust seals in place so I would remove both of them.
Now, as you no doubt have some symptoms of wear? There are 5 "important" bearings in the box (2 on main shaft, 2 on layshaft, plus sleeve gear bearing) do you think you might need to replace all of them?
There is some info. available on the forum on replacement of the layshaft bearings and sleeve bearings, also on aligning the drive side oil seal. Just ask away of you need help.
I have suffered from getting the sleeve gear bearings wrong, but at the 2nd attempt I seem to have got it right without the need to involve a machinest or buying expensive reamers etc.
