You have two different files fileA and fileB containing similar records (one record per line), and you would like to remove the records that fileB contains from fileA (subtract) producing a new file (fileC) that contains only records that are contained in fileA with records from fileB removed.
Use the following grep command
grep -vxf fileB fileA > fileC
You want to use ldapsearch to search from a file (file contains domains and ldap contains emails), but you want to suppress empty output lines (option -LLL does not seem to suppress them).
Use grep -v ‘^$’ like
ldapsearch -LLL -H "ldaps://ldap_url:nnnn" -D "cn=Directory Manager" -w $LDP -b "ou=ou_name,dc=domain,dc=com" -s sub -f denyDomains.txt "(mail=*@%s)" uid mail status | grep -v '^$' > denyDomainsResults.txt