- First you need to retrieve your picklist field using package.xml. For example:
- Once you retrieve add <isActive>false</isActive> tag with the values that you want to deactivate. For example:
- Now again deploy your picklist field and the values that you marked as isActive false will be shown in the deactivated values section
- If you want to see how to retrieve and deploy picklist field after changes you can check the below video
SFDCWallah 
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