IP instances or cells on the BD are in-memory objects. That is a copy of the instantiated IP is created in memory, but it is not written to disk until you save the BD.
As can be seen in the following figure, as cells (IP) are instantiated in the block design, they do not appear in the Sources window under the BD. At this point all cells or IP objects are created in-memory. The same applies to Hierarchical IP or IP Subsystems. The IP and the related files, such as BDs underneath IP subsystems, sub-cores, and so forth, are not written to disk until you save the BD. After you save the BD, the Sources window is updated to show all the IP under the BD hierarchy as shown in the following figure.
After saving the BD, if you delete an IP from the BD canvas, the Sources window shows the IP sources with a “?” icon. This updates after you save the BD. (See the following figure.)