I agree with Terry, but I'd add a couple of things: First the bike doesn't calculate partial charge cycles like you did. Every time you recharge it from less than full, it simply adds one. So your five short cycles add up to five, not one.
But it's okay, because as Terry points out, "2500 cycles" refers to FULL cycles, from full charge to full discharge and back again. That's pretty much the WORST thing you can do to a battery, other than overheating it. What you're doing, short cycling, is much more gentle on batteries.
When the Toyota Prius first came out, people were very concerned about the cost of replacing the battery, saying it was going to cost a fortune every 50,000 miles. But the engineers designed the system to only charge the battery to 60% of capacity, and only discharge it to 40%. That only gives you 20% of the capacity of the battery to use, but it extends the life of the batteries immensely. There are many Priuses running on their original battery packs with 500,000 miles on them, still working perfectly. Don't be afraid to use the full battery capacity, but if you want to extend the life of the battery, short cycles (and managing temperature) are the way to do it.