To answer the original question, if you have a hardware debugger and can access the chip with it, you can disassemble enough to find the EEPROM writing code and set a hw breakpoint there. Configure the breakpoint to automatically resume and use it to count the number of times that code is executed. If fusing prevents access, see if you can find a copy of the binary/hex/elf file that gets programmed and program it yourself to a blank device using the debugger, then find the EEPROM write code and count using a breakpoint. If it needs to run on the actual board just reflow your own unfused and accessible one onto it.