Upgrading an OTA ticket
 

Can I upgrade an OTA-bought Economy Flex fare online, or only through an EK agent? Or not at all?
Don't see why I shouldn't be allowed to but sometimes the rules make no sense so best ask if anyone has any bad stories.

Are you talking about upgrading using cash or miles?
Cash: I think only the OTA can do it. The problem with any TA ticket is that the airline won’t touch it.
Miles: From experience you can do it on line or via the call centre. Caveat: I haven’t used a TA for many years, so it may have changed. Call centre (or live chat) might work better than Manage My Booking.

My bad! I meant with miles from Y Flex to J. The upgrade for my segment is currently available online. But i'm wondering if the upgrade can be done online later, because I believe the entire "Manage Booking' functionality is not visible to bookings made through a TA?

Some, but not all MMB functionality is available on TA bookings (seat allocations for instance are OK).
Why don’t you just try? If not successful, try the chat function on the website. Make sure you are logged in to your Skywards profile. I find the chat function very reliable and helpful.
Don’t wait until ‘later’, upgrades tend to disappear quickly!