When the SET command is used on the command line, the values you specify are in effect for only that session. They override values previously specified.
You can append the original value of the variable using %variable%. The following example would cause the ILIB environment variable to be set to the original value of the ILIB environment variable, with the /NOFREEFORMAT option specified ahead of any existing options.
SET ILIB=/FREEFORMAT %ILIB%