I may have found a workaround - by default the managesieve script is stored as .dovecot.sieve
Unfortunately, dovecot presents that as a mail folder - mail clients that are aware of managesieve ignore them but sadly eMc doesn’t 
By editing the /etc/dovecot/conf.d/90-sieve.conf you can change the default sieve filename (in my case, to dovecot.sieve), restart dovecot and eMc will, after an account delete/re-add sync again with no errors.
So there is a workaround but it would be nice if eMc allows manual subscribe/unsubscribe to mail folders rather than me having to make a global action that affects all the domains a users on the server.