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#1029 – Asset Table Feature
this is quite strange. LittleHelper first asks Joomla to clear the recycled items; if that fails, it then proceeds to delete assets and related articles. So either way the assets should get deleted.
Before deleting anything, a .sql backup file is stored in the /tmp folder; there you can see what was deleted and have a list of all the ids. Additionally, the deleted ids are stored in the error log.
I have made a note to check the delete feature, but it will be handled in approx three weeks as we're delivering a large project now.
This will not solve your issue though; as I understand you still have tons of assets that match nothing: those can be removed with a lot of caution with direct database access, use something like this: select the third word in the dot-separated asset column 'name', i.e. the article id, and LEFT JOIN the articles table (#__content), and select the ASSETS that have no corrensponding article. The selection substring is repeated for your convenience
SELECT a.id AS ASSET_ID, a.name, SUBSTRING_INDEX(SUBSTRING_INDEX(a.name, '.', 3), '.', -1) as articleId, c.id
FROM `#__assets` AS a
`#__content` as c
ON c.id=SUBSTRING_INDEX(SUBSTRING_INDEX(a.name, '.', 3), '.', -1)
WHERE a.name like '%content%' and a.name like '%article%' AND isnull(c.id)