This is what Sage Support had told me about the tracking. Of course we will believe it when we see it!! Sage 100 tracks the number of unique employee IDs during tax calc. It keeps a list of employee IDs (that never resets) and compares against that during tax calc to see if you are over your tier. This counts for all companies so if you run tax calc as a test in a backup company (or run PR out of multiple companies) those will get added to the same ongoing list and counts each unique employee ID. If you fire someone or they leave, Sage indicated this won't count towards the tier as long as you mark the employee as terminated.
Regarding the fix that just was emailed to customers, the notes say it will only prevent future problems. After the fix is installed, do the following to correct previous renumbers.
** NOTE** This program fix is only to prevent the issue from happening in the future.
If you have already exceeded your tier:
1.Install the Program Fix
2.Renumber the current employee back to the original Employee #
3.Then renumber again to the current Employee #
If you continue to run into issues after following these steps please contact support