Publishing an item that is stored in resources, for example, in /sitecore, might result in the deletion of all non-resource items in the target database. This happens if the target database contains an item version that overrides the resource item, for instance if the /sitecore item was edited in the target database.
To resolve the issue, upgrade your instance to Sitecore 10.3.
To mitigate the issue, run a cleanup command on the target database to delete the items that override the default resource items. For more details, refer to: