It seems unlikely that the upgrade had anything to do with the missing records as the file format from filemaker 7 to 11 is unchanged.
I suggest investigating other possible causes.
Perhaps the records were already missing and you only now spotted their absence?
Any scripts that delete record that might go awry?
Any cascading deletes defined in your relationships?
Are your field indexes OK? (a corrupted index can keep finds and sorts from working correctly and this can make records appear to be missing because they couldn't be found.)