I’ve seen this happen on several client customer lists and have not received a satisfactory answer from Intuit as to why it occurs. It can, however be rectified.
To re-populate the customer list with the missing customers you will need to rebuild the data file. To do this, from the File dropdown, select Utilities and Rebuild Data. You will be prompted to make a backup copy of the data file prior to the rebuild. Once the rebuild is complete, check to see if the missing customers have been re-populated. Sometimes this rebuild has to be done a few times for it to work.