Revert to El Capitan
Next time I'll remember to set my POP3 server to keep mails for a month before I ever upgrade again :/

Simplest solution seems to have been to re-clone back from my two-week-old El Capitan clone - the one I made right before the upgrade.
That successfully took me back to El Capitan - but from 2 weeks ago.

That left me with having to remember/pick through what had been changed in the past two weeks.

Carbon Copy Cloner makes a Safety Net folder containing older versions - though in this case it was more useful for finding newer versions of apps I'd updated in the meantime.
Mainly what it had dumped in there was "Sierra".

My most important stuff was my photography folder, so I simply copied that in its entirety from a safety copy [yesterday's Sierra clone].

A Parallels VM I knew I had been working on I did the same.

Because Mail had changed its library structure I lost two weeks of relatively unimportant emails - I can live with that.  If I remember anything hugely important I can boot to my Sierra clone &amp; forward it to myself.
Time Machine proved to be completely useless in that respect. It claimed to be able to restore missing emails, but as everything in the past two weeks was in a newer format, it couldn't actually find anything.

So, job done. It actually took about 45 mins in all; once I'd figured out the structure &amp; the potential sacrifice.

The moral of the story... sometimes two clones &amp; two complete backups still isn't enough to get back all data.

I'm still open to alternative suggestions.
I'm in a position to simply repeat the process, as I still have copies of all the 'originals'.