we have 8900 records in jos_content and 14400 records in jos_redirection. my guess is that the content table has had records deleted that were not also removed from the SEF table.

is there a way to regenerate the entire SEF table so they are synchronized?

Order Number: 00003401

Hello,
basically that can be, becouse from 1 content item, more then 1 URL can be generated.
If you did not enter metadata for your URLs manually you can simply purge the records and JoomSEF will regenerate them. If you do not modify the settings, they should be generated same as before.

Also you can cleanup them using URL editor viewer by deleting all unused with hits e.g. < 10 (50). Just filter the records and use "delete all filtere function".