I highly recommend that you reach out to your trading partner to inform them that you are only fulfilling part of the order, this way they can confirm if they are still interested in receiving the order.
If you only intend to fulfill part of the order you can create a PO Acknowledgement with an 'Acknowledgement Type' of 'Acknowledge - With Detail and Change'. This would allow for you to enter in what portion of the order you are able to fulfill, this can then be sent to your trading partner so they have a record of what you intend to ship.
You can create a partial shipment document that would only display a partial shipment of the original order. You would achieve this by creating a shipment document as you normally would, however, you would only pack the items that you would intend to ship. This would generate a shipment document and labels that reflects the items that you are sending to your trading partner rather than the entire order.
Please let me know if you have anymore questions. Thank you for using Support Center!
Best, Adam Lund SPS Commerce Infinite Retail Power