OK, we have been using the V1 API to date.
There is a V2 API and I have had a rpm in smetest to use this for some time and all my servers are on the V2 APi now.
https://bugs.contribs.org/show_bug.cgi?id=10595 (main work)
https://bugs.contribs.org/show_bug.cgi?id=10636 (small bug fix)
yum --enablerepo=smetest install smeserver-letsencrypt
smeserver-letsencrypt-0.5-3.noarch.rpm
dehydrated-0.6.2-13.el6.sme.noarch.rpm
By default it *should* remain using the V1 API and you will carry on as normal.
To change to the V2 API you need to set a key:
config setprop letsencrypt API 2
or
config setprop letsencrypt API auto
signal-event console-save
You then need to run dehydrated again.
I'd like to push this out reasonably soon, but I am sure there will probably be some breakages etc so please test it if you can and let me know via here or the bug tracker.