It may be necessary to clean up an attempted installation of Patch 3 if an error is encountered. If this situation occurs, future attempts to install the patch will fail unless this procedure is followed.
Remove the base_dir\saml2 directory.
This directory contains the SAML v2 binary bits.
Remove the following SAML v2 related properties from the bottom of AMConfig.properties.
com.sun.identity.saml2.am_or_fm
com.sun.identity.saml2.xmlenc.EncProviderImpl
com.sun.identity.saml2.xmlenc.SigProviderImpl
com.sun.identity.common.datastore.provider.default
Remove the appropriate Access Manager or Federation Manager staging directory and extract new one.