JBoss EAP 7.4.15 have removed duplicated .jar files in the virtual filesystem, which affects classgraph scanning.
See the following cases for more information:
https://issues.redhat.com/browse/JBEAP-25677
https://issues.redhat.com/browse/JBEAP-25881
As a result, custom EJB Modules can no longer be scanned with classgraph.

By the looks of it, the issue lies here:
https://github.com/classgraph/classgraph/blob/latest/src/main/java/nonapi/io/github/classgraph/classloaderhandler/JBossClassLoaderHandler.java#L116

Where "(File) classpathOrderOut.reflectionUtils.invokeMethod(false, root, getPhysicalFile")" returns
"/usr/jboss-eap-7.4/standalone/tmp/vfs/deployment/deploymentc5c5d28878f37435/my-custom-module.jar-b6085cefd724c425/contents"

And final File file = new File(physicalFile.getParentFile(), name) resolves to:
"/usr/jboss-eap-7.4/standalone/tmp/vfs/deployment/deploymentc5c5d28878f37435/my-custom-module.jar-b6085cefd724c425/my-custom-module.jar".

Notice the file path, where the duplicated module have been deleted. It can no longer be found at that location.