Some people collect whistles in various boxes and bags of a certain amount. They'll produce whistles until they collect a bag of 500. This requires you to keep track of whistles in a certain package, but you really only have that one package to track. Use a sticky note, make a text file on your computer or phone, just track it somehow. Then, when you end up with 5 bags of whistles, you'll know you have 2500 whistles.

One printable helper that may help is Whistle Counting Tray for Micro Bitonal Whistles by The Broken Circle if you use that particular whistle model.