The batteries on the Mini 2 have a memory as far a the number of charges to any one battery.
That being said, if the batteries are just topped off ( from say 96%) to get 100% flight time, does it count toward the number of times charged?
Nope. A charge is from 0% to 100%. Partial charges add up to a single charge. Two 50% charges are one full charge. 25 charges from 96% count as one charge?