There are basically 2 options when upgrading FDM classic to FDMEE: rebuild all artifacts, or use FDM to FDMEE migration utility to migrate some, then build the rest. FDM to FDMEE migration utility is a helpful tool but it has its limitation, for example, the utility can not translate script from VB script to Jython.
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Please refer to the utility doc for the details the utility can and can not do. The not applicable type of artifacts are those existing in FDM but not in FDMEE anymore.
When running the migration process, analysis will be needed when error out. Therefore you need to balance the overhead with the help it can do for you. Setting up the utility, doing troubleshooting do cost time.