Just out of curiosity: why did you send invoice before you shipped? (the customer had to prepay for item?)
Suggested steps to perform:
[you may need to refer to online help for further details]
Did you create a purchase order for the item? [not described]
If so, modify to reflect changed item, otherwise create purchase order for new item.
Unapply the payment from the sales invoice [go to customer ledger entries select payment line and select Unapply...]
Create a credit memo for the original sales invoice [you can select Cancel on the posted invoice to automatically create a credit memo]
Post it [do not send to customer yet]
- you customer now has an open balance of 1750 [I'm excluding GST from numbers here]
Create a new sales order with new item.
Assuming you now wait until you have received and shipped the new item..
Receive the new item on the purchase order
[Post] Ship the order or ship & invoice [depending if it's a one- or two-step process] - but do not send invoice to customer yet
Go to Customer
Select Ledger entries
Select the payment and apply to the new invoice, post the application - check remaining amounts: invoice is now partially paid
Print customer Statement (- will show your customer that his balance is 249 (new invoice - payment [I'm excluding GST from numbers here]
Send Credit memo, Sales Invoice and Statement to customer.
[Unfortunately Financials cannot print a "Partially paid" marked invoice, so your customer has to be told they need to pay the balance as per Statement.]
Post the purchase invoice when you recieve it from vendor, pay when due.