I know this is a super-old thread but it's one of the top hits when you look up "Delete All Flex Markers", so I thought I'd post the answer.
I was trying to flex a bunch of grouped and phase-locked stems but came across the problem that Logic places a load of flex markers for you when you first turn Flex on. So if you're trying to tighten the whole group a bar at a time everything following your manual flex stays locked where it is - unhelpful in this situation. Reset flex edits command doesn't delete them, just resets their position. Solution is to get the Eraser tool and drag it over all transients, erases them all in one sweep. Make sure to do it on the region, not the region header, otherwise will delete the whole region.
Hope this saves y'all some time!