After you update the server to 1.9.4 when trying to connect by BungeeCord (latest) throws from the server and the console displays an error:

[15:45:39] Netty Epoll Server IO #1/WARN: An exception was thrown by a user handler's exceptionCaught() method while handling the following exception:
java.lang.NullPointerException
at net.minecraft.server.v1_9_R2.NetworkManager.close(NetworkManager.java:247) ~[Spigot.jar:git-Spigot-4af49dc-23da8b0]
at net.minecraft.server.v1_9_R2.NetworkManager.channelInactive(NetworkManager.java:106) ~[Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:233) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:219) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.handler.codec.ByteToMessageDecoder.channelInactive(ByteToMessageDecoder.java:228) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:233) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:219) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.handler.codec.ByteToMessageDecoder.channelInactive(ByteToMessageDecoder.java:228) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:233) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:219) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:233) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:219) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.ChannelInboundHandlerAdapter.channelInactive(ChannelInboundHandlerAdapter.java:75) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.handler.timeout.ReadTimeoutHandler.channelInactive(ReadTimeoutHandler.java:144) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelInactive(AbstractChannelHandlerContext.java:233) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelInactive(AbstractChannelHandlerContext.java:219) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.DefaultChannelPipeline.fireChannelInactive(DefaultChannelPipeline.java:769) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.AbstractChannel$AbstractUnsafe$5.run(AbstractChannel.java:567) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.util.concurrent.SingleThreadEventExecutor.runAllTasks(SingleThreadEventExecutor.java:380) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.channel.epoll.EpollEventLoop.run(EpollEventLoop.java:268) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:116) [Spigot.jar:git-Spigot-4af49dc-23da8b0]
at java.lang.Thread.run(Thread.java:745) [?:1.8.0_91]