Letsencrypt renew issue after last update

I have virtual server was working fine with letsencrypt renew every 3 months but after last update for Virtualmin 5.07 the update doesn’t work and the expire date is stuck at:
Mar 24 16:54:00 2017 GMT
The (Time since last renewal 3.08 months)
When I press Only Update Renewal doesn’t have any error but the date still at same Mar 24 and it’s already Expired.
Can anyone please help me.

Update: All virtual servers has the same problem the renew button doesn’t work and doesn’t update the certificates.

I also had an issue after some virtualmin update with let’s encrypt renewal :
Virtualmin added “mail.mydomain.com” in the “Domains associated with this server”
I had to remove it to make let’s encrypt work again.
If it does not solve the issue, share the error mail you received when renewal failed

How did you remove the added associated domain as i couldn’t.
alsot this problem is that mail.domain.tld i have add it as virtual server so i can use the SSL for it now with new update it’s in 2 virtual server the main domain.tld and another virtual server named mail.domain.tld

Go to virtualmin -> server configuration -> manage ssl certificate -> let’s encrypt
Here you have “Domains associated with this server”
Check “Domain names listed here” box below, copy the domains associated from the line above, without the mail.domain.tld

Then update renewal

I have another solution for this (mail.domain.tld) is to remove the virtual server i have created for it’s own and update the main domain that contain the sub domain mail.domain.tld and this will work fine.

Couldn’t it be possible to a have the possibility in the global config to choose if the mail.domain should be added to the “Domains associated with this server”?
Having lots of sites on the server it is a pain in the #@2*£ to have to change all of them manually…