mymodule_file_replace_entity_presave.php

<?php

use Drupal\Core\Entity\EntityInterface;
use Drupal\file\Entity\File;
use Drupal\node\Entity\Node;

/**
 * Implements hook_entity_presave().
 * @param \Drupal\Core\Entity\EntityInterface $entity
 */
function mymodule_file_replace_entity_presave(EntityInterface $entity){
  if ($entity->bundle() == 'file') {
    $uploaded_filename = $entity->getFilename(); # UPLOADED FILENAME

    # If File is Uploaded then Stash the Entity for use later
    if ($uploaded_filename){
      # STASH THE UPLOADED ENTITY INTO A SESSION VARIABLE
      $tempstore = \Drupal::service('user.private_tempstore')->get('mymodule_file_replace_fileupload');
      $tempstore->set('file', $entity);
    }
  }
}

/**
 * Implements hook_entity_update().
 * @param \Drupal\Core\Entity\EntityInterface $entity
 */
function mymodule_file_replace_entity_update(EntityInterface $entity) {
  if ($entity->bundle() == 'resource') {
    $tempstore = \Drupal::service('user.private_tempstore')->get('mymodule_file_replace_fileupload');
    $file_stash = $tempstore->get('file'); # UPLOADED File Entity

    if ($file_stash && $file_stash_entity = File::load($file_stash->id())) {
      # Get the Uploaded File Name and the URI of the uploaded file
      $file_filename = $file_stash_entity->getFilename(); # UPLOADED File Name
      $file_old_uri = $file_stash_entity->getFileUri(); # UPLOADED File URI

      # Build the new file path from the old path parts
      $path_parts = pathinfo($file_old_uri);
      $new_file_uri = $path_parts['dirname'] . '/' . $file_filename;

      # Check to see if the name was changed during upload to avoid a collision on the filesystem
      if ($file_old_uri != $new_file_uri) {
        $overwrite = TRUE;

        # Query all 'file' entities for the filename that was uploaded and stashed in filereplace_entity_presave
        $query = Drupal::service('entity.query')
          ->get('file')
          ->condition('uri', $new_file_uri, '='); # URI of file we want to Overwrite
        $file_query_ids = $query->execute(); # Execute the query

        # LOOP Queried Entities that matched the URI of our Stashed Entity
        foreach ($file_query_ids as $id) {
          $query_entity = File::load($id);
          $references = file_get_file_references($query_entity);

          if ($references) {
            # Loop the file's referencing entities
            foreach ($references as $field_name => $field_references) {
              foreach ($field_references as $entity_type => $type_references) {
                foreach ($type_references as $id => $reference) {

                  # IF THIS FILE IS REFERENCED BY AN ENTITY OTHER THAN THE ONE WE ARE EDITING - DON'T OVERWRITE
                  if ($id != $entity->id()) {
                    $node = Node::load($id);
                    $url = $node->toUrl()->toString();
                    $path = file_url_transform_relative(file_create_url($file_old_uri));
                    $overwrite = FALSE;
                    drupal_set_message(t('File could not be overwritten because the filename is in use on <a href="@node_link">@node_title</a>. New version uploaded instead at %filepath.', ['@node_link' => $url, '@node_title' => $node->getTitle(), '%filepath' => $path]));
                  }
                }
              }
            }
          }
        }

        # Overwrite the File
        if ($overwrite) {

          # OVERWRITE THE FILE AND UPDATE/SAVE THE ENTITY
          file_unmanaged_copy($file_old_uri, $new_file_uri, FILE_EXISTS_REPLACE);
          $file_stash_entity->setFileUri($new_file_uri); # Set the new Entity URI
          $file_stash_entity->save(); # Saves the Entity
          drupal_set_message(t('Original file %file overwritten with new one.', ['%file' => $file_stash_entity->getFilename()]));

          # CLEANUP TEMPORARY FILES THAT WERE RETURNED IN THE QUERY ABOVE
          foreach ($file_query_ids as $id) {
            $query_entity = File::load($id);

            # REVERT THE URI AND DELETE THE FILE
            if (!$query_entity->get('status')->value) { // If status is temporary
              $query_entity->setFileUri($file_old_uri); // set the old entity fileURI to the temp URI
              $query_entity->save(); // save the updated URI
              $query_entity->delete(); // delete the temporary files
            }
          }
        }
      }

      # DESTROY THE ENTITY STASH
      $tempstore->delete('file');
    }
  }
}