They will be fine as long as the cells are the same manufacturer, size, type and quality (based on how many times they have been charged/discharged), the controller will see them as one 8000 mAh 5S pack. You should be fine, as the cells will discharge in unison.
And to be sure of the equal discharge of the batts - if possible use a battery balancer - to make sure all the cells in both packs are the same voltage... Happy running....