Starting with the switch to JLine 3, pressing Ctrl+D at the jshell tool prompt causes (tested on Fedora 27) --
Exception in thread "main" jdk.internal.org.jline.reader.EndOfFileException
at jdk.internal.le/jdk.internal.org.jline.reader.impl.LineReaderImpl.readLine(LineReaderImpl.java:564)
at jdk.internal.le/jdk.internal.org.jline.reader.impl.LineReaderImpl.readLine(LineReaderImpl.java:404)
at jdk.jshell/jdk.internal.jshell.tool.ConsoleIOContext.readLine(ConsoleIOContext.java:200)
at jdk.jshell/jdk.internal.jshell.tool.JShellTool.getInput(JShellTool.java:1238)
at jdk.jshell/jdk.internal.jshell.tool.JShellTool.run(JShellTool.java:1174)
at jdk.jshell/jdk.internal.jshell.tool.JShellTool.start(JShellTool.java:975)
at jdk.jshell/jdk.internal.jshell.tool.JShellToolBuilder.start(JShellToolBuilder.java:254)
at jdk.jshell/jdk.internal.jshell.tool.JShellToolProvider.main(JShellToolProvider.java:120)