Those books you mention aren’t considered inspired by the Holy Spirit, or included in the Canon of scripture but were often included for historical and moral teaching. Nobody removed them from the Bible.
It was for rather shaky reasons that some rejected these books as being part of the Bible. Luther also was tempted to exclude the book of James and the book of Revelation - he ultimately kept them but seemed to have remained critical of them - especially James. There was a church long before there was a Bible as we know it today.