We have run a Black Duck Scan against the R 11.3.6 SP7 installation and it has come back with High Vulnerability identified as below.
Apache XML Xalan-Java 2.7.0 apache-xmlxalanjava 407664 CVE-2014-0107 High
The file in question, xalan.jar, is located here:
The file xalan.jar is only used for EEM Migration between 8.4 to 12.0. Since EEM is already upgraded and working you do not need the EEMigrate folder. You may safely delete it.