Running a discovery from the WLC Manager runs a discovery on all WLC and also sets the enableAPDisc on associated Cisco_LWAPP_App models back to “Yes”.
Check if enableAPDisc has been set to “Yes” on the WLCs associated application model and make sure to not run the WLC Manager discovery after setting this attribute to “No”.
If you don't need any AP being discovered, another option is to set to No the
VNM Information tab > Autodiscovery Control > Modeling and Protocol Options > Create Wireless Access Points
How can I disable discovery of Access Points on individual WLCs in Spectrum
How does the WLC Manager discovery in Spectrum work ?