Yes, you can have your employer withhold less city taxes, and for the current tax year (2017) you can file a return to get some of the money back.
It is best to keep a log of when you do go in the office versus working from home.
http://kcmo.gov/tax/tax-home/forms/tax-form-descriptions/ Link for below and the Form is at the link also.
Form RD-109NR is a schedule used by a non-resident of Kansas City, Mo. to request a refund of tax withheld based on the fact that the employee had whole days worked out of the City. The number of days worked out of the City must be verified by the employer. Form RD-109NR is also used by a part-year resident of Kansas City, Mo. to determine earnings attributable to their period of residency.
