The following procedure assumes that you want to change ALL the properties that belong to X to new percentages. (Normally you would need to go and change each existing property one-by-one) - but there is another way.
Create a dummy agent with 0% commissions for everything. (Let's call that agent Dummy)
Then do a Change Agent All from agent X to agent Dummy (You do this under Tools, Options - Advanced, Change Agent All). All properties under agent Dummy now set to 0% commission.
Make sure that agent X is setup with the new commission rates (Let's pretend its 10%)
Then do another Change Agent All from agent Dummy back to agent X. All properties under agent X now set to 10% commission.