B787 flight crew reported after takeoff they got an EICAS message for brakes after selecting gear up. They decided to return to the airport.

Narrative

We were operating flight ABC to ZZZZ scheduled at XA:35. We were informed that our aircraft would be swapped and flight would subsequently be delayed until XB:45 so that ZZZZ1's flight ABD could take our aircraft for their already delayed departure. The information we received was that the ZZZZ1 plane was having issues being towed to the gate due to Maintenance not being able to get the brakes released because of a malfunction. So our aircraft became the one with the brake issue and waited until Maintenance was able to clear the event before we could depart. We then received two additional delays; one stating an ETD for XC:30 and the next was XD:15. The issue was cleared by Maintenance sometime around XB:40 and the aircraft began tow to [gate] XX. We began pre-flight and boarding as normal; got the release and pushed back and began our taxi out around XD:20 with no noticeable brake issues the entire time. We taxied and departed XXR from [Taxiway] 1 at ZZZ around XD:30. The Captain; who was pilot flying (PF); called for gear up and as I did so; the gear sounded like it was having issues coming up into the wheel wells followed by a dull grinding noise and eventual 'thud' once the gear appeared to be fully retracted. Around 700 ft AGL as we began our initial assigned turn to the north; we got an amber EICAS message associated with a checklist that said 'BRAKES'. We waited until we got to a safe altitude before diving into the checklist (sometime after 18;000ft and our relief pilot stepped out of the flight deck). The checklist seemed to provide two possible issues; either brakes were still engaged or there was a failure with the brakes/monitoring system but regardless; autobrakes may not operate and/or degraded braking on landing could result. We also noticed around this time the aircraft wrote up two separate entries pertaining to the brake malfunction. Just past ZZZ [VOR] around 35000 ft the Captain transferred the radios and aircraft to me while he contacted dispatch and Maintenance Control. The information Maintenance Control provided us was fairly ambiguous as he claimed that indeed the right side MLG brakes were showing engaged to a degree but possibly not enough to cause a skid or tire lock up on landing. We also had conflicting information from Dispatch stating 'no weather at the time of our arrival in ZZZZ' but as the Dispatcher was reading that off; my weather apps were showing chance of light-moderate showers at our now delayed time of arrival into ZZZZ. The Captain was not able to get anything more than a 'maybe; maybe not' type result with how the brakes may function at our destination airport and grew skeptical just as I did. After he hung up with Dispatch and Maintenance Control; both the Captain and I went through the entirety of what we felt could compromise safety should we continue this flight. We concluded that based on the conflicting weather information at the time of our arrival into ZZZZ; the uncertainty of what the brakes might actually do once we touch down in ZZZZ and the possibility of having to divert to an alternate enroute (ZZZZ1 showed rain and ZZZZ2 with shorter runways as our ETOPS alternates); the compounding collective crew fatigue as the duty day wore on; we found ourselves increasingly concerned about compounding issues should we need to divert to anywhere else in along the route for anything else and now having to figure out the brakes on landing whether it be ZZZ; ZZZZ or anywhere else. As a crew; we arrived at the decision that returning to ZZZ where we are well equipped with Maintenance and gate resources and a 13;000ft runway with sufficient emergency equipment was the safest move to make. As the Captain and I informed Dispatch and ATC of our intentions; we began our turn back to ZZZ for landing. I maintained both flying and radios while the Captain called the purser up front and gave him the full brief and rundown of the situation. ZZZZ [Center] gave us a clearance back to ZZZ [VOR] tojoin the ZZZZZ X back to ZZZ and we set up our fuel jettison procedure to be able to land below MGLW back at ZZZ as soon as the relief officer returned up front. We descended to FL340 where we basically stayed as we jettisoned fuel starting before ZZZ [VOR]. In all; approximately 50K lbs of fuel needed to be jettisoned prior to landing. The Captain then took the controls back after the arrival had been briefed and all appropriate checklists had been completed. The relief officer and myself continued to search for and record non-normal landing distances should the brakes not function properly and because we intended to conduct the landing without the use of autobrakes as a precaution per the first 'BRAKE' checklist advisory. We [requested priority handling] with ZZZ [Center] and maintained '[priority] status' all the way with ZZZ Tower. We also requested Runway XXR as it is the longest at ZZZ and also requested emergency equipment standing by as an additional precaution. The Captain flew the visual approach to XXR and we touched down just prior to the 1;000 ft markers. As soon as we touched down; we felt a quick but hard tug to the right (likely the brakes on the MLG) but then a release as soon as the Captain input left rudder and began manual braking. We pulled off the runway without incident and came to a stop on Taxiway 2 short of 3 so that emergency crews could do an inspection of the MLG prior to taxi back to the gate. We were given the all clear by the emergency crews and they followed us all the way back to XX. Once parked at XX; we debriefed with two Maintenance technicians in the flight deck about what we saw and experienced through the event. Nothing further was noted after completing our termination checklist as normal.