@Dawn Dockrill 

I know this reply is kinda late...

"I understand the FIFO process but why doesn't removing inventory (taking it to 0) and then changing the unit cost and receiving inventory back in doesn't change the unit cost?"

It changes the inventory valuation of that item, which is what matters.  If you make an inventory adjustment to zero out an item and then receive the item back using an Expense transaction at the desired cost, your asset value of the inventory item is the new cost.  Keep in mind, the "unit cost' field of an inventory product doesn't update and isn't used to determine the value of on-hand inventory.  It's just used to pre-fill the cost field when you purchase the item. 

"If I remove 600 books at $2.49/bk and then change the cost to $5.02 and receive 600 books in the new unit cost should be $5.02. "

What do you mean by "unit cost".  The unit cost field on an inventory product is just used to pre-fill the cost field when you purchase an item.  It doesn't change when you receive items because it's not used to determine inventory value.  The 'Rate' and 'Asset value' on the inventory valuation reports are what are used to determine inventory value.  Zeroing out an inventory item and receiving them back at the new, desired cost will update the Rate and Asset value.