There is an option in Orchestrated to put an invoice on "hold" by creating what's called a Payment Block.
To block/hold an invoice, click on the Accounting tab of the invoice and then the drop-down for "Payment Block":
If one doesn't exist, click "Define New" and fill in the Payment Block Reason on the window that pops up:
You can then attach this block to the invoice and this will be omitted when running through the Payment Wizard.
When it comes time to remove the block, simply pull the invoice back up and uncheck the box next to "Payment Block" on the accounting tab.