Does Canvas drop the lowest score for external assignments based on points or percentages? 


Regardless what point each external assignment has in the external system, when it is shown in Canvas, it is set to be out of 100.  That is the value that would be used by Canvas when you decide to drop the lowest score. You can choose to ignore the lowest score for a student, but please note this option is available only for an assignment group, so it would drop the lowest score within that group. You would need to set that up for multiple assignment groups, based on how many external assignment types are in the course.  

Please review this guide for setting an assignment group rule that includes ignoring the lowest score for the individual group.