This is fine. If you have an onward boarding pass, you're fine. Nothing special will happen and you'll just present your boarding pass as usual and board your flight and enjoy, you know, the exciting onboard United product and the wonders of civil aviation in the 21st century. It happens in transit as your itinerary and e-ticket get updated at different paces as you continue flying.
You might have a problem if
(1) you manually used united.com to 'cancel check-in' for some masochistic reason, or if
(2) united.com no longer shows the upcoming segments on your flight (flights that you have not yet flown are not visible on the UA web site), or if
(3) the coupon status associated with your e-ticket for the coupon that covers the flight you are currently taking is not "Flown" after at least an hour in the air.
Otherwise there is no problem.
With old pre-merger united.com I used to accidentally do (1) every now and then by trying to change my seat using OLCI; back in the day, OLCI would sometimes say "hey, you're trying to check in within X minutes of your flight, that is past the departure cutoff, you are gonna miss your flight so I have helpfully cancelled your check-in and you can contact an agent for help!". Then I would walk over to the gate with my boarding pass and say with shame, "um, can you please check that I'm still checked in? I just have a HUNCH that something has gone wrong". I think I managed to do this twice, lol. It's no longer possible to do this on accident with new post-merger UA systems.
Even (2) can be okay — I have had that happen in a weird case where I did a semi-manual SDC with an agent's help and my reservation ended up out of sync between the reservations system and departure control system, which I didn't think was possible with United, but it totally is. I was a little freaked out but even that was fine.