Please treat this urgent as Management wants accurate information
Then you need to open a support ticket. Social forums like this provide best effort support and are not for urgent issues.
How do I clean the SCCM database with all the UDA information and start from scratch.
There is no direct method to remove all UDA info. You will have to script this using the RemoveSourceMethod of the SMS_UserMachineRelationship WMI class. See https://learn.microsoft.com/en-us/mem/configmgr/develop/reference/core/clients/manage/removesource-method-in-class-sms_usermachinerelationship.
Other than disabling the UDA in client settings, do I have to do anything else so that the manual information we feed in does not get over-write by automatic method
What exact permissions we should give to "service desk team" in the SCCM console just to do user device affinity manually ( both via file and one-by-one )
For RBA, there's an entire class named "User Device Affinities".