B787 Captain reported GPS spoofing occurred and the flight crew only had one usable GPS that had a time delay.

Narrative

I was part of the relief crew flying the second portion of the ZZZZ - ZZZ leg. We came up to take over the flying duties approximately 7 hours into the flight. Flying crew briefed us that they had flown through the area of spoofing with the GPS's turned off and on as prescribed in the bulletin. When we took the airplane; they were logged on to CPDLC; on course but only had a single GPS navigation. During the flight; we lost CPDLC communication and was unable to log on until just prior to the oceanic crossing. The second GPS came back for a short period time and then failed for the remainder of the flight. It should be noted that the clock had approximately 3:05 minute discrepancy between the Captain and FO's clocks. After contacting Maintenance; we could not choose a GPS receiver nor choose the correct time for ATC communications. ATC was receiving our position reports consistently 3:05 behind our actual time; i.e; crossing a coordinate actual time of arrival XA:00; reported XA:03. Due to the solar storm; HF communications were very difficult and unintelligible. We just clarified with ZZZZ [Center] and ZZZZ1 [Center] that we were single GPS and the times could not be adjusted; but were consistently 3:05 off. They were agreeable with the discrepancy and we continued as filed. CPDLC worked normal except for the time discrepancy and changing from controller to controller sometimes required a manual change. The remainder of the flight was under radar control and was normal.