I have this problem this morning also.. three games left three ships in battle with no battle reports or XP accrued. Logout/login back in did not fix this problem, neither did restarting game client.
Very frustrating - it worked fine last night! I am scared my whole fleet will sink, like what actually happens in war....
[ NOTE - Completely restarting, even the game launcher/loader, did cause my ships to reappear in port, but no record of the three battles (2 wins) is evident: no XP, no credits, no challenge/mission credit]
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Oh, finally, it has been carefully determined empirically and anecdotally that, for all intents and purposes, that this SUCKS.