I see exactly what you describe, for one site, web search shows 73 of 78 pages, UK only last week showed 12 and the last few days zero, across a bunch of sites I see similar issues.
The funny/strange thing is, the UK results that showed up until a few days ago was canonicaly damaged, the site does have valid 301 non-www to www and index is sorted too all nav is to full URL's and the site shows up in the correct order with site: tool on the web results.
The root/ was there but in 4th place behind some other root pages but also behind some very deep content, 4 directories deep.
All sites are .co.uk and hosted in the UK, 2 sites are .org.uk and hosted in the US, same problems, on one of the sites I added about 30 pages, within days they were performing well then bam, all supplemental and MIA in the UK search.
I was suprised nobody (until now) has mentioned this, its been ongoing for around 4 weeks, that's when I first noticed the problem, and it doesn't seem to fit in with the other currently discussed filtered/penalised threads.
How long can it last?