It feels like there must be a better approach, but the blunt instrument way is to split the result of the left side join and leave only left or right side values in each of the pipes, then filter nulls from the right side, and merge. Something like this (assuming lhsPipe has values from File_A, and rhsPipe has values from File_B):
Fields lhsFields = new Fields("lhs-id");
Fields rhsFields = new Fields("rhs-id");
Pipe joinPipe = new CoGroup(lhsPipe, lhsFields, rhsPipe, rhsFields, new LeftJoin());
Pipe lhsValid = new Pipe("lhs-valid", joinPipe);
lhsValid = new Each(lhsValid, lhsFields, new Identity(new Fields("id")));
Pipe rhsValid = new Pipe("rhs-valid", joinPipe);
rhsValid = new Each(rhsValid, rhsFields, new Identity(new Fields("id")));
rhsValid = new Each(rhsValid, new FilterNull());
Pipe result = new Merge(lhsValid, rhsValid);