Hey Wei,
I'v been backing and forthing with the good folks at arcitecta outside of this thread and they've been a great help. I had missed that the "content missing" was an asset.query option, and they suggested it, too. Thanks to both parties!
We found that if the query asks for ":action get-value :xpath content/url", it chokes on the first failure so you don't get the whole list. If, however, it asks for :action get-meta, it succeeds, so we're able to get the whole list of missing assets. Just knowing the item number of the asset is enough to infer its path in the filesystem and move our investigations to that side
We're currently in the process of trying to sort out how/when the assets' content was deleted, and we're think we're getting there.
Scott