I think it depends on the airline?

I just witnessed someone encounter this problem on Tuesday. We were on an AA flight from CLT to MSP which ended up being diverted to ORD due to weather, with the flight rescheduled for ORD to MSP the following day at 9am. While I was sorting out a hotel reservation in the waiting area, I was overhearing a very frustrated pax loudly pleading with the poor gate agents they sent down to help with logistics that they needed to be in MSP to catch a connection at 6am also on American, but the gate agent couldn't do anything about re-arranging that flight or help with re-booking to the final destination straight from ORD because the next-day connection ticket was on a different PNR and still locked by Expedia and they would have to make changes by calling them.

The other risk you take with portal bookings is that you are introducing another billing system in the middle between you and the airline, and it's possible for that to get badly out of sync.

Just a few examples from Reddit:

A flight cancellation on the airline end resulted in the rescheduled flight going unpaid by Chase travel, leaving the traveler with a useless reservation and a check-in agent powerless to help: https://www.reddit.com/r/CreditCards...but_didnt_pay/

or Chase not actually booking a change, resulting in a last minute scramble: https://www.reddit.com/r/CreditCards...vel_is_insane/

Or even with Amex, trying to use credit from cancelled flights leads to hours of frustration: https://www.reddit.com/r/amex/commen..._on_the_phone/