You mean 16-bit overflow? I can "guess" that in the PC. With my sample rate I don't expect increments higher than 10-20 units between following samples
NO, I do not mean 16-bit overflow and your sampling rate has nothing to do with it. You seem to indicate that you are using the µC to count and you will fail.
If an encoder stop right across a boundary, you can get 100s of counts starting at several MHz without anything moving unless you use the HP chip or a CPLD.

Erik