The writer prolly believes in the multiverse or alternate realities. Maybe that’s how Chiaki’s device worked? Who knows? I suspended my belief enough because it was a good story to let it slide.
While I laid awake in bed this morning (yes, I know…), a thought occurred to me regarding the counter reset. The device must have a limitation built in that if all of the counters are used and someone travels back and visits the owner of that counter, it will reset to 01. Chiaki had used his last counter to save his friends. So, Chiaki’s was at 00 just like Makoto’s was before Chiaki went back.
Chiaki went back and Makoto’s counter reset to 01 where his was 00. Then, Makoto went back and Chiaki’s counter reset to 01 where hers became 00.
This is to prevent “further” exploitation of using the device to get back counters. Does that fly?
This is just my rambling and not based off anything official.
Thanks all! I watched this last week after seeing this thread. What a great movie!
IMO - Whenever we see Time Travel in fiction it is best not to make assumptions and just allow it to be a plot device. In this case we don’t see any evidence of other dimensions/realities so it should just be one time line. To travel, one has to leap and the intensity?/duration?/height? determine how far back it is. It also appears that you fall back into your own body, hence all the gymnastics and why there are never more then one of you.
My opinion is that no counters were restored. Chiaki went back in time to a point where Makoto still had 1 leap. When she realized it she leaped back to a point before he used it to steal the bike, told Kousuke not to use the bike and then told Chiaki what she knew and how she felt. In the end she follows in the aunts footsteps and spends her life taking care of the painting. Maybe he gets another charger and comes back for her or perhaps he goes to different girls through time and manipulates them into preserving the painting into his time. I prefer the former. 
Your counter explanation is valid. Hmm…