Bridging code from Field Collection patched with earlier patches that provided revision support (ones that used item_id). Pick and choose the update logic that you need in your use case.

mymodule.install.php

/**
 * Fix up the field collection tables in anticipation of update 7001. If this
 * doesn't work as an update, do it as a utility page.
 */
function mymodule_update_7006() {
  // Add the archived column
  $archived_spec = array(
    'description' => 'Boolean indicating whether the field collection item is archived.',
    'type' => 'int',
    'not null' => TRUE,
    'default' => 0,
  );
  db_add_field('field_collection_item', 'archived', $archived_spec);
  return "Prep database for field_collection_update_7002().";
}

/**
 * They went back to using value instead of item_id for the field schema.
 */
function mymodule_update_7007() {
  $value_spec = array(
    'type' => 'int',
    'not null' => TRUE,
    'description' => 'The field collection item id.',
    // Set default to 0 temporarily.
    'initial' => 0,
  );

  // Update the field_collection_field_schema columns for all tables.
  foreach (field_read_fields(array('type' => 'field_collection')) as $field_name => $field) {
    $table_prefixes = array('field_data', 'field_revision');
    foreach ($table_prefixes as $table_prefix) {

      $table = sprintf('%s_%s', $table_prefix, $field_name);
      $item_id_column = sprintf('%s_item_id', $field_name);
      $value_column = sprintf('%s_value', $field_name);

      // Add a value column.
      $value_spec['description'] = 'The field collection item id.';
      db_add_field($table, $value_column, $value_spec);

      // Initialize the value to be the same as the item_id.
      db_update($table)
        ->expression($value_column, $item_id_column)
        ->execute();
    }
  }
  return "Prep database for field_collection_update_7002().";
}

/**
 * Drop the now-irrelevant item_id column to make debugging code that was using
 * the old structure easier. Also drop field_name from
 * field_collection_item_revision and add the index.
 */
function mymodule_update_7008() {
  db_drop_field('field_collection_item_revision', 'field_name');
  db_add_index('field_collection_item_revision', 'item_id', array('item_id'));
  foreach (field_read_fields(array('type' => 'field_collection')) as $field_name => $field) {
    $table_prefixes = array('field_data', 'field_revision');
    foreach ($table_prefixes as $table_prefix) {
      $table = sprintf('%s_%s', $table_prefix, $field_name);
      $item_id_column = sprintf('%s_item_id', $field_name);

      db_drop_field($table, $item_id_column);
    }
  }
  return "Drop field_name from field_collection_item_revision, index item_id,
    add foreign key, and drop item_id columns from Field Collection field
    tables.";
}