Hmm, I don't know. That's in the regional tab in preferences. I would assume that it's giving you that warning because once you change something it does affect other invoices. For example, if you change the headers to say something different, (such as Ship Date instead of Invoice Date), it doesn't change it from this point forward, it changes it for any invoice you look at, including old ones. In this case, the only way I know of to save an invoice exactly the way it was is to save it as a pdf.
But you're talking about pricing here. Again, I don't know, but based on what I just said plus your warning box, it will probably change the pricing structure for all invoices. This would throw off some of your records by a few coins, which could add up depending on how many invoices you already have. You would probably have to then go in an manually change those invoices back to what they were.
Make sure you backup your data before playing around with it! Have you tried contacting customer support?
Anybody else have any input?