Have you tried doing something like:
a, b, c, a&b as key
sql select a, b, sum(c) as c from file1
group by a,b
having sum(c) > 0;
d, e, f, e&f as key
sql select d,e,f from file2;
Think that should work for you but not sure about order of load, think it will execute first load fully (with the having clause) and then join to the second load. the "key" field is the field that QlikView will use to join on.