I found that the issue can be solved by removing the file .metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.ui.workbench.prefs
from the workspace.
The file contains perspective IDs as keys, and a XML structure as values. Removing a single line of this file that refers to a perspective solves the problem for that perspective.
I noticed that the perspectives were referenced by their short name (without the package) before, and with their fully qualified name after the new release. So there must be some side-effect when using the old prefs causing the handlers do not work anymore.