How do I save iBooks pdf on iPhone to computer so I can delete them from iPhone?
To delete them only from your phone, follow these steps:

In the upper-right corner of the iBooks window, tap Select.
Scroll to find the item that you want to delete, then tap it.
In the upper-left corner of the iBooks window, tap Delete.
Tap Delete This Copy.

If you tap Delete from All Devices, it will remove it from iCloud, which will cause it to be deleted from all devices (including your computer).