You can do that from the Time Entries screen by selecting the entries and clicking Actions > Batch Update. On the Batch Update dialog, there is an option to update the invoice number. Note that this option is only visible when you are viewing the time entries by project. So make sure to select Project in the Show drop-down of the screen before using Batch Update.
Note: Batch updating the invoice number of entries is used for Progress Billing in Core. You cannot use it for the entries that you have already invoiced. Check out this article for details: How to attach time entries to an existing invoice.