The manager and the folder contain different things
Kodi introduced core Video Extras with v21 for movie-library bonus material such as interviews and alternate endings. Its manual distinguishes removing an Extra from the manager from deleting a file on storage. If the same interview reappears after Update Library, first confirm that its file remains in the movie’s Extras folder. Do not assume the earlier manager action failed to save.
Read the counterintuitive scan setting
The documented Ignore video extras on scan setting determines whether a discovered Extras folder populates the movie’s Extras listing. The manual warns that its enabled state does not itself provide a blanket exclusion from ordinary movie scraping; unwanted bonus files may need the documented exclusion configuration. Review the relevant instructions before changing an existing advancedsettings.xml file, and preserve that file rather than replacing unrelated settings.
Check the version and one movie folder
Core Extras requires movie folders rather than a flat collection. The manual also records a v21 scanning bug and a v22 fix, so capture the installed version when a correctly placed folder is not recognised. A small check can use one authorised movie and one bonus item: confirm the folder location, the scan policy and the resulting manager entry. Choose whether you want the Extra listed before removing it again. A manager cleanup is not a request to erase the underlying bonus video.
Questions, answered
Does Remove in Extras Manager delete the bonus video file?
The official manual says it does not; a later scan can rediscover that file depending on the settings.