If the print and fax flags are disabled on the customer record (and only email is enabled), then when attempting to print multiple invoices (say a batch), those customer invoices will not get printed. There is no override for multiple invoice printing - you'd have to enable the print flag on the customers, or print them one at a time.

You could use a trick to help with this - search for customers from the SmartFinder who don't have the print flag on, then export this list to Excel. You can use this file to import just the customer number, and 'skip' all other fields. Set a default value for the print invoice to 'True' - setting the print value for all customers. (the print the invoices to paper). Then do the same import with the same file, setting the default value to 'False' this time - setting the print value back to Off for just those customers.