Let's Encrypt invalid challenge only for one domain

Hello

We are facing an unusual issue while setting up Let's Encrypt certificate. We have one main domain (eg: maindomain.com) and multiple parked domains (eg: parkeddomain1.com, parkeddomain2.com, subdomain.parkeddomain3.com, etc.), and we have to setup a single SSL certificate for all these domains using SAN. Once in a while, we may have to add new parked domains to this main domain, and thus, we have to regenerate the certificate by including this new parked domain.

We were successfully able to do this process till now, but now when we added a new domain (eg: newparkeddomain.com), the certificate generation fails always with the message:

Getting challenge for maindomain.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for parkeddomain1.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for parkeddomain2.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for subdomain.parkeddomain3.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for parkeddomain4.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for parkeddomain5.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for subdomain.parkeddomain6.com from acme-server...
Waiting for domain verification...
Challenge is valid.
Getting challenge for newparkeddomain.com from acme-server...
Waiting for domain verification...
Challenge is invalid. Details: Invalid response from http://newparkeddomain.com/.well-known/acme-challenge/r0W-YpkLxgpnqwQHmdpDe5i82AMY7mri0q_lLhobejE: . Exiting...

Can anybody let us know what could be the problem related with this newparkeddomain.com? As the certificate generation is failing, all other domains which was working fine with HTTPS, also fails to load. Then we have to restore the backed up configuration files and restart Apache to make them work.

We are stuck with this issue for quite a while and were trying all possibilities which we could think of. So any inputs regarding this is highly appreciated.

FYI: we already have enabled Alias /.well-known in the configuration file

Thanks & Regards
Sujith