When I change a commission plan, does it change all of the items associated with that plan?

No. When you make an adjustment to the commission, eBay fees, invoice fees or anything else on the commission plan, those changes do not apply to items that are already under that plan. The changes will apply to items you take In Queue after saving the Commission Plan.

If you want the changes to take place, you must click “Apply changes to existing items for which no check has been cut” under Admin > Commission Plans.