the bearings are housed inside the case, they might be frozen to the shaft. when you pull the chaincase out the bearings come with it.. if you're positive you have all bolts off and anything that might be holding it on, then that is probably the case. try to keep the case aligned with both top and bottom, don't take one side off too far or it will get misaligned and the axles wont slide easily out of the bearings.
If this happens to me I usually take a rubber mallet and pound on the end of the shaft that is giving me trouble, while holding a long screwdriver or skinny prybar behind the chaincase, trying to pry it out as i pound the shaft.
If this happens to me I usually take a rubber mallet and pound on the end of the shaft that is giving me trouble, while holding a long screwdriver or skinny prybar behind the chaincase, trying to pry it out as i pound the shaft.