With the release of version 5.5 edition, the Customer Number change module is now free, so I'm sure there are many people taking advantage of it.
I was at a client yesterday who had over 9000 customers and 9 years of transaction history in AR, and my tests were showing that the customer number change would take around 65 hours to complete. Using the MSSQL profiler, I saw that the choke point was the ARPJD table, it was taking 30-35 seconds to change each customer number.
Solution? Add an index on IDCUST to the ARPJD table. The 65 hours of processing time went down to 12, which meant we could run it overnight without disrupting the business. Make sure you take the index off when you're done, it could interfere in a future upgrade.