Magento 2 supports custom source models for attributes except for indexing them into the
table (which feeds layered navigation).
The original problem is found in
\Magento\Catalog\Model\ResourceModel\Product\Indexer\Eav\Source:302 where it ensures
that the values saved exist in the
eav_attribute_option table. When using that custom source model, those values do not
The first / easy solution is to comment out those lines. That doesn't work for production so a more durable
method needs to be had. While using a
preference is not preferrable, this will solve the problem in the short term.
After some research and many hours spent, I found that @maderlock has a good fix: https://github.com/magento/magento2/issues/417#issuecomment-265146285
Here is how to get this running:
composer require fidesio/attribute-index-fix
php bin/magento module:enable SwiftOtter_AttributeIndexFix
php bin/magento cache:clean