I am trying to extract some custom content that was installed, then later the original file was deleted/lost - there are saves where it is in use, and those work, but it can't be used in any other new games (unfortunately, the game was reinstalled between these events and trying to find the content, so i can't just get it from the cache). I have taken a look at the files, but haven't been able to work out anything about their structure. Is there any way to recover custom content that was in use when a save was created?

CC is not saved with a game. I just checked a save of mine and there are no items there that could be extracted from the *.nhd file. And you won't find them in the caches either. The only way to get them back is to re-download the items.