When dumping a dynamic CDS archive, we skip unlinked classes from custom loaders. The reason is:

We cannot link these classes during dynamic dump time -- linking may require more classes to be loaded, which would cause user-supplied versions of ClassLoader::loadClass() to be called.

Since dynamic dump happens at VM exit, executing such user-supplied code at this stage may cause unpredictable behavior.
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Since JDK-8261090, we can store old classes in the static archive. These classes are unlinked, and will be linked/verified at runtime. We should extend this mechanism to support unlinked classes in the dynamic archive.