FlexiMerge seems to be a valid solution to this problem : 

class BypassMerge[A, B] extends FlexiMerge[A, FanInShape2[A, B, A]](new 
FanInShape2("BypassMerge"), OperationAttributes.name("BypassMerge")) {
  def createMergeLogic(p: PortT): MergeLogic[A] = new MergeLogic[A] {

    val readA: State[A] = State[A](Read(p.in0)) { (ctx, input, element) ⇒
      ctx.emit(element)
      readA
    }

    val readB: State[B] = State[B](Read(p.in1)) { (ctx, input, element) ⇒
      readB
    }

    override def initialCompletionHandling = CompletionHandling (
      onUpstreamFinish = { (ctx, input) ⇒
        ctx.changeCompletionHandling(defaultCompletionHandling)
        readA
      },
      onUpstreamFailure = { (ctx, _, cause) ⇒
        ctx.fail(cause)
        SameState
      }
    )
    override def initialState: State[_] = readB
  }
}

  "Bypass string source with more element" in {
    val p = FlowGraph.closed(Sink.publisher[Int]) { implicit b =>
      import FlowGraph.Implicits._
      sink =>
        val merge = b.add(new BypassMerge[Int, String])
        Source(List(1,2)) ~> merge.in0
        Source(List("1","2","3","4")) ~> merge.in1
        merge.out ~> sink.inlet
    }.run()


    val s = TestSubscriber.manualProbe[Int]
    p.subscribe(s)
    val sub = s.expectSubscription()


    sub.request(10)
    s.expectNext(1)
    s.expectNext(2)
    s.expectComplete()
  }




  "Bypass string source with less elements" in {
    val p = FlowGraph.closed(Sink.publisher[Int]) { implicit b =>
      import FlowGraph.Implicits._
      sink =>
        val merge = b.add(new BypassMerge[Int, String])
        Source(List(1,2,3,4)) ~> merge.in0
        Source(List("1","2")) ~> merge.in1
        merge.out ~> sink.inlet
    }.run()


    val s = TestSubscriber.manualProbe[Int]
    p.subscribe(s)
    val sub = s.expectSubscription()


    sub.request(10)
    s.expectNext(1)
    s.expectNext(2)
    s.expectNext(3)
    s.expectNext(4)
    s.expectComplete()
  }



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