Multi-valued attributes in an LDAP object must have unique values, that is, each value of a multi-valued attribute must be different from any other value of the attribute in that object. No structuring of an LDIF input can change that.
I have seen applications remove all values of the multi-valued attribute, then add the desired (in this case, there are no multi-valued attributes). In some cases where the multi-valued attribute is required by the object class of which the group is a member, the entire group can be removed and then added back.
Obviously, #1 is a substandard solution (though it can be made a little more palatable by using LDAP transactions wherein the group is removed and added as part of a single transaction, but this may not be available, the world being full of low-quality servers and APIs that do not support transactions). The LDAP client would do better to retrieve all the members of the group, then, with that knowledge, add only the attribute values that are not already in the group.