As mentioned already they are applying fare rules:
"WHEN A TICKET IS ISSUED WITH COMBINATION OF FARES WITH DIFFERENT PENALTY RULES THE MOST RESTRICTIVE CANCELLATION RULES WILL APPLY FOR THE ENTIRE TICKET"
This happens for most of airlines I think and not only QR, rules unfortunately are not well advertised but just reported in the middle of the very long fare rules list. To save money it was better to change the return date only till the maximum validity of the ticket and change it again when return date already fixed, as only return leg Flex involved no fee would have probably been requested.
CS agents are most of the time not competent and never give the right information or advise.
In similar situations the best solution is probably to buy two one way tickets with required restrictions or a full flex return, whichever is cheaper.