This is sort of an old thread but the only one I found when I had this problem. I could not get my price rules to work either once they updated to the new invoice format. Talking to QBO rep and just by chance got it to work for us. What I did that may help some of you save the frustration later, it may not work for you but it did for us.

1st open an invoice - chances are you are using the old format that is now not compatible with the price rules any more.

2nd Click the "update invoice" to switch to the new invoice format, for us it kept kicking us out every time I tried. It got really frustrating for a few but if you click that then hurry and hit another button with in the new invoice format prior to it kicking you out then you should be able to save and update and everything will work. This must be a glitch with in the update, not really sure. 

The new format is different and it will get some getting use to, but however it should fix your problem if you are having the same issue as we did. I did tell QBO rep that they should look in to that and get the word out so that no one will have to deal with it as we did, and obviously several others as I have, as I have been reading through the feedback here. Good Luck.