In WordPress, when you edit images using the Image Editor, only core sizes are saved, and not any of your custom sizes (including post-thumbnail!). If you register image sizes using the functions in this Gist, images edited in the Image Editor will be saved in all image sizes.

add-image-editor-size.php

<?php
/**
 * If you register image sizes using the function below, images
 * edited in the Image Editor will be saved in all image sizes.
 *
 * @see https://core.trac.wordpress.org/ticket/19889
 */

if ( !function_exists( 'add_image_editor_size') ) :

    function add_image_editor_size( $name, $width = 0, $height = 0, $crop = false ) {
        add_image_size( $name, $width, $height, $crop );

        add_filter( "pre_option_{$name}_size_w", function() use ( $width )  { return $width;  } );
        add_filter( "pre_option_{$name}_size_h", function() use ( $height ) { return $height; } );
        add_filter( "pre_option_{$name}_crop",   function() use ( $crop )   { return $crop;   } );
    }

endif;

if ( !function_exists( 'set_post_thumbnail_editor_size' ) ) :

    function set_post_thumbnail_editor_size( $width = 0, $height = 0, $crop = false ) {
        add_image_editor_size( 'post-thumbnail', $width, $height, $crop );
    }
    
endif;