In KONTAKT 5.0.3, Native Instruments introduced a new plug-in migration feature for the AudioUnit platform. When opening an old host project in which either KONTAKT 2, KONTAKT 3 or KONTAKT 4 were used, KONTAKT 5 is automatically instantiated instead if the original plug-in version is not found. All the instruments from your host project will be loaded into KONTAKT 5. Currently auxiliary tracks do not migrate properly and are crossed out in the host's mixer when migrating a Logic project containing a multiple output instance of KONTAKT. We are in contact with Apple to address this issue in a future Logic Update.
The workaround is as follows: After recalling a session with disabled auxiliary tracks, press the "-" button next to the fader to remove these tracks. Once you have done this, press the "+" button to recreate them. The assignment is now correct and the auxiliary tracks are no longer crossed out, Please note that the auxiliary channel names displayed in Logic will display the plug-in name of the KONTAKT version originally used in your song (in this example, KONTAKT 3).
Note: any FX chains on the Aux tracks need to be stored beforehand by the user and then loaded back into the respective track to recreate the original sound. An easy way to do this would be to save the setting as a Logic Channel Strip preset to recall it afterwards.