Open the discovery log file and check if there is information message or warning message about the project being ignored and the reason why it is ignored. Navigate to the page Delivery Manager Tool - Discovery - Warning to check the type of message that may lead to this behaviour.
Check if the issue is linked to the DMT Configuration :
Open the config.DmtDiscovery file for the two versions of the delivery and compare them. The result will be as shown below:
In the above example, a discoverer has been unselected : The discoverer is Java files per package folder.
Compare the 2 DMT : For this example, in the DMT we can see that the discover has been unselected as shown below, compared to the previous version.
Check all the differences between the two versions. Check also the plugins used. To do that, in the Delivery folder, go to the Version level for the two versions, and open an *.entity.xml file (same name for both version) and compare the discoverer version installed as below : The part to take into account is : If there is differences, it may explains the reason why there is removed projects.
If none of these steps help to resolve the behaviour, contact CAST Technical Support and provide Relevant Input to help CAST Technical Support team investigate and solve your problem.