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I guess it all depends on the relative importance of the keywords and landing pages.  If the pages that were hit are important landing pages that drive conversions it should be something that is addressed.  If the pages are being penalized, on-page optimization probably won't help too much; however, building quality back links could have some benefit.

It's possible that rankings have decreased on certain pages because the links that were helping the pages rank are no longer valued, rather than the pages receiving direct ranking penalties.  If this is the case than building some quality links to replace the ones that are no longer valued may help the pages rank well again.

What worries me the most is when you say the company is going to switch to "white hat only for a few months" (not exactly sure how you meant it, so forgive me if I read into it wrong).  Things are never going to improve if white hat tactics are only a temporary strategy.  Google is only going to get better at picking up shady tactics.

Adding the following lines to the bottom of your robots.txt should do it:

Sitemap: http://www.example.com/sitemap/uk/sitemap.xml

Sitemap: http://www.example.com/sitemap/de/sitemap.xml

If you wanted to update the file names to be different it wouldn't hurt, but I don't think you would have any problems with how they are currently set up.  If you have submitted them to WMT and they are being picked up ok I think you are fine.

Take a look at the text-only cached version of the page.  If you are unsure how to do that follow my crude instructions below.

What I do to test if Googlebot can view the content of my homepage:

Do a Google search for 'site:example.com' and find your homepage.  Next to the green URL in the SERP listing for your homepage there is a green arrow.  Click that and select 'cached'.  Then, when viewing the cached version of the homepage, click 'Text-only version' in the bottom right corner of the grey bar that appears at the top of the browser.

If the content you are questioning shows up, there is a good chance Google has obviously been able to crawl and index it.  If the content is not there, there is a good chance they can't.  If the content is in a hidden div it will likely still not show up in the text-only cache.

I've found this as a good source in the past, not sure if you have already checked it out:

http://www.internetmarketingninjas.com/blog/search-engine-optimization/301-redirects/

High Domain Authority.  Quality back links.  Good user engagement.

So did commercial.vigilantinc.com/wine-refrigerators.php have a 301 redirect to vigilantinc.com/commercial/wine-refrigerators.php; or did you just have one redirect from commercial.vigilantinc.com to vigilantinc.com/commerical thinking it would also redirect all the subfolders?

If the latter is the case you need to put a 301 redirect on every subfolder of the subdomain, or place a site wide redirect on the subdomain.

Were the redirects tested and working?  I'm confused why Moz would not be picking up the redirects.  Do you have any specific examples of the pages that Moz was reporting as duplicate content?

Is it possible you just redirected the root of the subdomain, rather than every page on the subdomain?

I think it's something that should definitely be addressed.  The massive amounts of broken links, and subsequent loss of link equity, could have a more negative impact on your site than the Moz errors that were being picked up.

If auto-tagging wasn't turned on, were the campaign URLs manually tagged?  Did they have utm parameters on them?

It is most likely a case of not having any campaign tags on the destination URLs.

I'm working on a site where dynamic URL extensions to the homepage were automatically redirecting to the regular homepage URL.  Though autotagging was turned on in Adwords, the campaign tags were being lost in the redirects meaning that the paid visits were not being tracked properly in Google Analytics.  They were being recorded as organic visits.

Double check that the destination URLs of the PPC campaigns are not redirecting, and that any autotagged URL will not redirect.

Do a site:examplesite.com to see if Google is able to identify individual sections of content on the site.  If not, you need to create pages to have something to work with.

With only one landing page you can really only target a couple keywords.  I think you should definitely focus on building out landing pages for the content, rather than having it all display at one URL.  Without landing pages you really can't target a variety of keywords.

Thanks for the response!

I do see that message, which is kind of what confused me. I saw the "We've already migrated at least one of your existing campaigns over from PRO" part and assumed I should be seeing some data.  I have used up all of my campaign slots currently so I can't create a new one.  I just received access to the beta yesterday so I will give it a little more time to update.

I believe Moz had some issues with their linkscape index sometime over the past few months.  The metrics for the last update were put together using a smaller sample size of links, meaning the numbers were down across the board for most sites.  The problems were corrected and now the metrics are being calculated using a larger sample size of links, meaning the metrics went back up.

I've been invited to the Moz Analytics Beta; however, I am not seeing any data for any of my campaigns.  Do I have to do something specific to enable the beta, or does it take a while for information to appear?

There may be a plug in to place rel=canonical tags on the page.  Sometimes, when the plug in field is left blank, a self referencing rel=canonical tag is placed on the page.  I wouldn't worry about it too much, it shouldn't harm your site.

From: http://moz.com/blog/dispelling-a-persistent-rel-canonical-myth

"Looking through Google's blog post on the subject, this isn't explicitly stated. However, you can see that even the example website, Wikia, employs this practice on the page Google points out. You can also see Googler Maile Ohyeanswering a comment on this:

@Wade: Yes, it's absolutely okay to have a self-referential rel="canonical". It won't harm the system and additionally, by including a self-reference you better ensure that your mirrors have a rel=”canonical” to you."

In WMT click on the URL that is 404'd and then select "linked to from".  It will show you where Google is picking up the 404 error.

Are these 404 pages being linked to from an external site?  Sometimes the 404s that appear in WMT are from links pointing to your domain from an external site, often one that has scraped your site.

Check out this - http://moz.com/community/q/keyword-difficulty-showing-only-bing-search-volume-exact-match

It's possible that Google just feels that the text you have in your H2 is a more accurate description of your page.  Is your meta description too long?  I know that Google occasionally ignores the Title Tag and displays the H1 or other text in the SERPs if they feel it is more relevant.

The "Google US" means that they are analyzing the top results on Google to determine the keyword difficulty.

Google does not let people use their AdWords API (where Moz would pull search volume from) if they violate guidelines.  One of the guidelines was that you cannot scrape search results (which Moz does to determine Google US difficulty).  I believe the keyword search volume was switched to Bing  data work around this issue.  I do not believe there is a way to have the Google search volume display in the keyword difficulty tool.

Any one feel free to correct me if I got any of that wrong.

Is there a Duck Duck Go research tool?

I'm curious, what search data has been lost?