It has happened in recent seasons too. Only one set of games in the "wrong half" though.
In lower leagues I think in previous seasons sometimes the second half of fixtures has gone in reverse order. Somethnig along those lines might have happened in the Conference at least this year as for example Forest green played Newort home and away over the Christmas period. But I can;t be bothered to check.
Sorry to mention the Irish League again, but there, where teams play each other 3 times before the "split", there is a bizarre system whereby the first of the three round robins is NOT reversed. This can lead (and has led) to oddities where 2 teams can play each other on the same ground only a couple or so weeks apart.