Systemless root is the most recent development by Chainfire. The benefits of systemless root are several. It is easier to unroot (just a factory reset will unroot your device), easier to apply OTA (over-the-air) updates (just re-flash stock boot image to apply OTA update) and it will not soft brick your device, which is a frequent outcome of rooting.

Now, to fix apps do not recognize issue with Systemless Root, you only need to just issue the below commands one-by-one. However, you should first install a Terminal Emulator app from Play Store to issue the commands.

How to Fix Apps Don’t Recognize Systemless Root on Marshmallow Devices

  1. First, install a Terminal emulator app from Play store [HERE]. It is necessary to issue the command.
  2. Open terminal app and issue the command: su (if asked, grant SuperSU permission to access the app)
  3. Now, issue the below commands one-by one: mount -o remount,rw /system touch /system/bin/su mount -o remount,ro /system reboot 4. The last command will reboot your phone. Now, try an app that did not recognize root access previously. It should recognize and work fine (Source)