EntityFieldQueryException: Unknown field

I'm reopening issue #1866032: EntityFieldQueryException: Unknown field as it is not fixed.
I'm getting a bunch of these errors on each cron run since I deleted a Field Collection field:
EntityFieldQueryException : Unknown field : field_[...] in EntityFieldQuery->addFieldCondition() (line 841 in [...]\includes\entity.inc).
Besides, plenty of deleted data stay for ever in the database.