How to add/remove applications from "File and Folders" inside "Security and Privacy" -> Privacy Tab
Run
tccutil reset SystemPolicyDocumentsFolder
tccutil reset SystemPolicyDownloadsFolder
tccutil reset SystemPolicyDesktopFolder

They are case sensitive.
Sources:

https://www.felix-schwarz.org/blog/2018/08/new-apple-event-apis-in-macos-mojave &quot;Configuration Profiles&quot; section.
https://docs.microsoft.com/en-us/graph/api/resources/intune-deviceconfig-macosprivacyaccesscontrolitem?view=graph-rest-beta
https://github.com/chernandezba/zesarux/blob/873f31b9db563369039909d4d841e004fd77c443/src/docs/mac_os_catalina_users_permissions.txt
https://developer.apple.com/business/documentation/Configuration-Profile-Reference.pdf

If the above is too cumbersome,
tccutil rest

which resets all permissions across all profiles.
tccutil.py is outdated and even after disabling SIP, it will not give meaningful info about the database:
/Library/Application Support/com.apple.TCC/TCC.db


https://github.com/jacobsalmela/tccutil/issues/18#issuecomment-655420138