Magento – Magento2 – Filter product collection by SKU is not affecting layer navigation

You need to rewrite how Mage_Catalog_Model_Layer builds the attribute collection using the current product collection's attribute sets:

protected function _getSetIds()
{
    $key = $this->getStateKey().'_SET_IDS';
    $setIds = $this->getAggregator()->getCacheData($key);

    if ($setIds === null) {
        $setIds = $this->getProductCollection()->getSetIds();
        $this->getAggregator()->saveCacheData($setIds, $key, $this->getStateTags());
    }

    return $setIds;
}

For this context, you'll want to check the product collection for grouped products and return the attribute set IDs of grouped children. These are then evaluated in getFilterableAttributes():

public function getFilterableAttributes()
{
    $setIds = $this->_getSetIds();
    if (!$setIds) {
        return array();
    }
    /** @var $collection Mage_Catalog_Model_Resource_Product_Attribute_Collection */
    $collection = Mage::getResourceModel('catalog/product_attribute_collection');
    $collection
        ->setItemObjectClass('catalog/resource_eav_attribute')
        ->setAttributeSetFilter($setIds)
        ->addStoreLabel(Mage::app()->getStore()->getId())
        ->setOrder('position', 'ASC');
    $collection = $this->_prepareAttributeCollection($collection);
    $collection->load();

    return $collection;
}

You will likely need to deal with the cache key. I would develop with block caching off and then test extensively with it on.

The problem is getLayer is a singleton and holds afaik one collection. There is no easy way to achieve what you want. You can unset the whole collection (maybe) after doing whatever you are doing (which I didnt understand)