You're welcome, CHMM.

Since all of the previous numbers that have been used remain the same whether or not custom transaction numbers are turned on, there isn't a way for QuickBooks to automatically assign numbers from the beginning. 

You would need to manually change each number while having the custom setting turned on, and then turn it back off for the system to continue going in numerical order from the last entry.

I hope that clears things up a bit more. You know where to find me if you have any other questions.