You need to first talk to the employer and get this straightened out with the HR office.

None of your income should be taxed by IL.  You will need to get a letter from them stating that you lived and worked all year in KS, and then file an IL non-resident return with $0 income and get all the taxes paid in back from IL.

Then you will file a KS return and will owe KS taxes due to no taxes withheld.  I suggest you make estimated tax payments to KS so a year from now this does not happen again.