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In addition to DM/IM books, make sure you expand your business knowledge. Knowing how customers tick and how SWOT works rarely goes out of style.
My suggestions:
Are they linked to a page that the crawler can find?
What are you generating it with? Online tools like xml-sitemaps.com act like a spider - if they can't crawl from the homepage to the new page, they simply won't find it.
Internal tools, like a Wordpress plugin, should actually find those orphan pages.
I don't know if there's a way to do this in Moz but you could always get Screaming Frog & tell it to ignore robots.txt - that will definitely crawl it. You can check titles, descriptions, canonicals, H1s, etc. that way. It doesn't give the Moz level analysis but it's a start that def works. You can also see if you have parameter issues that way.
I understand client confidentiality - if you want to PM me the link to look at privately, I'd be happy to.
That being said, anchors finally get too high? Did losing 17k knock them WAY out of whack? (Anchor on the other links was 18%, now 35% or something?)
"links pointing to it are generated by a half dozen or so article based sister sites" = this could definitely be the issue as well. I have a few ideas but hard to tell without knowing just a bit more.
We've tested this a few ways.
Add map to the footer - seems to help somewhat. Not a big jump but definitely a boost.
Add map to the contact page along with the address - this helped the most in our testing.
Add map to any other page - no effect in our tests.
We tested 2 controls and 4 sites set each way = 14 total.
Of the 14, the 2 controls and the 2 "any other page" had very little improvement. The 8 on #1 and #2 had definite moves and so it does seem to affect the results. Putting the address on the page, along with an embedded G map was by far the best for us.