Differences in the way the ladder logic is constructed could mean that the preset for the counter might need to be some number other than 500 in order to time 1000 scans.
That's why I chose to count such a large number of scans. If your logic actuallly times 999 or 1001 scans, the average value will only be off by a fraction of a percent. There will be more variation from one scan to another than the variation introduced by the timer's ACC value representing the time for 999, 1000, or 1001 scans.
Remember, this is a procedure for calculating the average scan time. If you need the precise scan time for a specific scan, this is not the method to use. But congratulations to you for thinking deeply enough about the details to come up with that question.