Is there a way with drush or console to delete all active config with a certain prefix?
This isn't the greatest solution, but it does work, and also allows you to not have to execute a dozen steps/commands to register your migrations.

In my custom module where I'm creating migration sources/plugins, I added a .install file and implemented hook_uninstall().  In there I delete the configurations remaining manually.

&lt;?php

/**
 * @file
 * Contains my_module_migrate.install.
 */

/**
 * Implements hook_uninstall().
 *
 * Removes stale migration configs during uninstall.
 */
function my_module_migrate_uninstall() {
  $query = db_select('config', 'c')
    -&gt;fields('c', array('name'))
    -&gt;condition('name', db_like('migrate_plus.') . '%', 'LIKE')
    -&gt;execute();

  $config_names = $query-&gt;fetchAll();

  // Delete each config using configFactory.
  foreach ($config_names as $config_name) {
    \Drupal::configFactory()-&gt;getEditable($config_name-&gt;name)-&gt;delete();
  }
}


Note: You may need to clear cache after uninstalling for the changes to show before re-enabling the module.

If you want to remove them before you uninstall you can either run each line from hook_uninstall() implementation in devel/php, or you can run them via drush:
drush ev "\Drupal:;configFactory()-&gt;getEditable('migrate_plus.migration.xxxxxx')-&gt;delete();"
You will probably have to clear cache after removing all of them manually via drush as well.

If you'd like to just run a couple of drush commands to re-register your migrations, you can add this drush plugin file my_module.drush.inc to your modules' root directory, clear cache, and run drush mpc -y &amp;&amp; drush mcr my_module.  You may need to also run drush cache-clear drush for the commands to be come available.

Here's the code for the my_module.drush.inc file:

&lt;?php
/**
 * @file
 * Contains my_module_migrate.drush.inc
 */

/**
 * Implements hook_drush_command().
 *
 * Defines drush commands.
 */
function my_module_migrate_drush_command() {
  // Company update Dynamically
  $items['migrate-prune-configs'] = array(
    'description' =&gt; dt('Prune migrate configs.'),
    'aliases' =&gt; array('mpc'),
    'examples' =&gt; array(
      'drush migrate-prune-configs' =&gt; 'Removes migrate configuations.',
    ),
    'callback' =&gt; 'my_module_migrate_migrate_prune_configs',
  );

  $items['module-config-reset'] = array(
    'description' =&gt; dt('Resets default config for a given module.'),
    'arguments' =&gt; [
      'module_name' =&gt; dt('Module name'),
    ],
    'aliases' =&gt; ['mcr'],
    'required-arguments' =&gt; 1,
    'callback' =&gt; 'my_module_migrate_config_reset',
  );

  return $items;
}

/**
 * Callback for drush command migrate-prune-configs to prune migratin configs.
 */
function my_module_migrate_migrate_prune_configs() {
  //Confirmation will be Y/N when use type “y” the condition will be executed if not it will not
  if (drush_confirm(dt("Are you sure you want to remove migrate configs?"))) {
    drush_print("Removing.....");
    // Get all of the migration config names.
    $query = db_select('config', 'c')
      -&gt;fields('c', array('name'))
      -&gt;condition('name', db_like('migrate_plus.') . '%', 'LIKE')
      -&gt;execute();

    $config_names = $query-&gt;fetchAll();

    // Delete each config using configFactory.
    foreach ($config_names as $config_name) {
      drush_print("..." . $config_name-&gt;name);
      \Drupal::configFactory()-&gt;getEditable($config_name-&gt;name)-&gt;delete();
    }

    drush_print("Removed succesfully");

    return TRUE;
  }
}

/**
 * Reinstall default module's config files
 */
function my_module_migrate_config_reset($module_name) {
  if (!in_array($module_name, array_keys(\Drupal::moduleHandler()-&gt;getModuleList()))) {
    return drush_set_error(dt('Module @module_name not found.', ['@module_name' =&gt; $module_name]));
  }
  // Initiate config installer for given module.
  \Drupal::service('config.installer')-&gt;installDefaultConfig('module', $module_name);

  drush_print('Configuration was successfully reset.');

  return TRUE;
}


The code for resetting the module's configs was found in this issue on d.o.  I found that it doesn't work unless the configs are already removed, hence the first command to remove them.