[Cynthia, Prescott, AZ]

Yes, that part in the picture looks quite dead with that visable hole probably being where a root previously existed and can be cut off. But you do not want to cut off any living part of the stem. So, working from the bottom up and using a sterile tool, start cutting looking for when you reach living tissue. You can also start to cut off clearly dead roots, and work your way up the roots until you see living tissue in the cuts. Those roots coming out of the obviously dead stem can be pulled out of the basket. Looks like, as you pull all the dead stuff out, you may be able to reseat the plant in the basket or put it in a new basket without any set back. Topping is a process where most of the good roots are left with the lower half of the plant, causes a set back because of the loss of this portion of the roots, but this does not apply to your case. However, I don't think there is any relation between the loss of the base of the stem, probably from miscellaneous unimportant causes, and the leaf spotting.