Watering after re-potting won't hurt them, just don't over water either. I recommend using Yates Lush Houseplant or Tomato Food. Feeding promotes flowering. This is ideal since you don't have any of the chemical set-up that is common in tap water. Cacti water every week or so.
Winter is a time of dormancy for cacti so water atleast once a month.
The micro-organisms that cause these problems love moist conditions, so plants that have been overwatered are prime candidates for these diseases. If you water it the next time you look the stems and roots may have turned mushy and rotten. On the other hand if you notice the initial damage early enough, further damage can be prevented by placing the plant in a well ventilated, dry room and holding back on watering until development of the disease is stopped. Keep cacti and other succulents fairly dry, especially during the winter months when they are dormant and do not need much moisture. Scale insects are pesky and I am still having problems with them.