When we override a price on a product line for a quote, if we ever go back onto that product line to change anything like quantity, the price defaults back to its original price. You then have to amend the price again back to the special price, but it is easy to not know there was a special price or what it was and miss amending it again.
When a special price is put in, it should stay as put in and not revert back.
Thank you for your feedback, the reason it changes is because the calculated special price can change based on other factors such as quantity.
I can definitely see where you are coming from and I think maybe a popup/user option asking what you'd like to do would be best.