The system, updates, contribs installed etc etc SME 9.1 set up as server only; fully updated with no contribs currently installed.
OK
What caused the original problem
Moving data from a suspect portable HD - put simply, I didn't check carefully enough how much space I needed to complete the transfer to a new disk.

We all make mistakes. just some are worse than others !
What you did to 'fix' it
Moved the data back off the server drive to a new USB drive.
And absolutely nothing else ? Exactly what 'data' ? Just wondering why you have a server with mail, but no data. Was this an upgrade or something ? Just trying to make sure we get ALL the facts and history - the devil lies in the details usually... please spell out exactly what you were doing.
over 3900 files - I need to do some housekeeping on my email folder. 
Is that all ?
(On a side note, it is generally reckoned Thunderbird is happier when you keep under 10,000 per folder, so you are OK for now......)
see attached (from WinSCP)
Unfortunately it isn't that clear. But it looks like they are at least owned by user 'office' and as you say, you seem to be user 'tony'
I can see no error messages in /var/log/messages relating to IMAP or IMAPS.
OK
/var/log/imap/current
/var/log/imaps/current
As far as I can see in WinSCP, these directories do not exist on my server.
Sorry - was looking at the wrong server my end !
Can you use putty to get a command line ?
However /var/log/dovecot/current contains lots of the following:
2016-08-03 23:46:59.294408500 imap-login: Info: Login: user=<tony>, method=PLAIN, rip=46.xx.xxx.130, lip=192.168.200.10, mpid=5129, TLS
2016-08-03 23:47:00.373743500 imap(tony): Error: open(/home/e-smith/files/users/tony/Maildir/cur/1435849344.9590.main:2,Sa) failed: Permission denied (euid=5000(office$) egid=5000(office$) missing +r perm: /home/e-smith/files/users/tony/Maildir/cur/1435849344.9590.main:2,Sa, euid is not dir owner)
2016-08-03 23:47:00.373751500 imap(tony): Info: Disconnected: Internal error occurred. Refer to server log for more information. [2016-08-03 23:47:00] bytes=647/197804
Does this mean there is a miss-match between my logon ID and the file permissions?
That's a good guess....
I suspect that a change to the directory/file permission will not fix this.
And that is probably a bad one

Clearly something isn't right here.... you have neglected to mention something somewhere.
Here are a couple of lines from one of my servers for some mail of mine - my login is 'john':
-rw------- 1 john john 1203 Aug 3 23:00 1470258025.4751_3.esmith:2,S
-rw------- 1 john john 202612 Aug 4 00:23 1470262981.10135_3.esmith:2,Sl
-rw------- 1 john john 30326 Aug 4 01:34 1470267282.13332_3.esmith:2,Sl
So yes it look like your mail files and possibly directories have the wrong ownership.
The question is how did that happen ? Or were you a different user in another life ?
What about this showing us this from Putty (you really need to get to the command line to sort some of this):
cat /etc/passwd |grep -i tony
and
ll /home/e-smith/files/users/tony/Maildir
The situation is possibly fixable, but we really need to understand how you got there in case there are other issues.
B. Rgds
John