unfortunately that's the problem of ex TPE married segment tickets. Even if underlying "D" fares is available for both flight for POS of HK, the married segment "D" for POS (point of sale) Taiwan may not be available. Reason is simple, the ex TPE "married segment" D-fares are lot cheaper, so they don't release it easily. I would assume you are close to your flight date - i find that ex TPE availability is extremely good for 1mth out but closer to dates you start having these problems.

One thing i did was (refer my post earlier) I waitlisted seperately and somehow they both cleared seperately and I was good to go by "re-marrying both segments". I'm not sure how agent did it but I didn't question - it sound like unknowledable agent just went ahead to confirm underying segments on its own and force merger it... I didn't have problem at check in either and I dumped my last HKG-TPE segment.

thanks CX for all the arbitrage opportunity ex TPE once again. I know you read it.