There isn't a way to import a change to a customer without updating the entire customer record - which will then be replaced by what you import.
There also isn't any error checking on the field to prevent duplicate account numbers.
However, you can export your customer list to an IIF file, edit it in Excel, and then import it again. I believe the customer number is exported into the first of two NOTE fields on the customer record. I recommend trying this with a small number of customers first, making sure that everything you care about is preserved when the IIF file version of the customer record replaces the existing one as you import.
To do this, export the customer list to an IIF file, which is a a tab-delimited file, and then open it in Excel. Remove all but a few customer records and then change the NOTE value, save the file, and import it. Start at File | Utilities | Export | Lists to IIF files...
