My advice based on recent experience: give it time. We made domain changes and rankings tanked, only to recover. We made a major design change and rankings dived, only to recover. Give Google some time to assess.
Yeah, major design changes are painful. Google Webmaster Tools is currently warning me that we have over 100 404s on various URLs, because those pages simply got removed completely.
Actually most of those 100 are the same few pages, but Google indexed it a metric shit-ton of times, and then added each of them to the index, and THEN it penalised us for "spamming."
I came in, removed it completely, and set up a robots.txt so it couldn't happen again. But the penalties and 404s will take up to a year to completely clear out of Google's end.
Funnily enough Bing hasn't penalised the site at all, and we're the number 3 rank for relevant search terms on there (2nd page on Google).
How does having duplicate content on your domain give you a spamming penty?
And for a site thats been a round for a while only having 100 404's is low - most site owners are v bad at tidying up old defunct urls and using script kiddie platforms like joomla and magento dont help.
It sounds like the content got removed completely, so there should not be a URL (either old or new) for that content.
It's true that they should have used 301s or rel=canonical or something in the past, but that also sounds like the least of their past problems, if I'm reading the parent comment right. Right now, I don't think they'd be much better off with 301s to a single URI that 410s instead of just directly serving 404s for everything, even though the 301 to a 410 is more right in some abstract sense.
