Yes, the value amounts in the original items database file are in the base value silver. So a value of 2.5 is 2 silver and 5 bronze according to the money heirarchy. If you have nothing below it, I'm not sure how it will handle that. I would assume you will lose the .5 so I'm thinking it would be best not to have any floating points (or fraction values) making them all "full" integer values. In reality that's how your world will probably look at change anyways. That's is here in the States we have a penny but we don't have a half-penny and all prices do not reflect the half-penny. If the penny were removed we would have to make sure all prices are divisible by 5. I would expect you would have to do the same in your world.
You database fix is a great way to go. Yes, when you update the database it should ignore your file. All the setup does is copy files over, it doesn't delete anything. So your new file will remain in tact. You will just have to change the item.xml file, as you thought you would, every time you update. This is another great way to make a database change. In fact I think I might promote this idea as a way to make a more specific xml change. Thanks for sharing that idea.
Thanks for the feedback and thanks for the enhancement requests. It's always great to see people using AutoHARP in ways I never thought of.
edit: No Bronze pieces? My goof. I'll enter a ticket for that.