In our end it's working properly. Some accounts were switched to Sectigo, but others not, as Sectigo seems to be too busy. After applying script, returning to Let's Encrypt and run AutoSSL for all users, remaining accounts seems to be SSL protected again.
BTW, affected server is a cPanel v86 with CentOS 6.
I am running the same, but for some reason the script didn't seem to do anything for me - an AutoSSL run still returns errors:
9:48:15 AM ERROR TLS Status: Defective
Certificate expiry: 12/30/21, 7:07 AM UTC (89.93 days from now)
ERROR Defect: OPENSSL_VERIFY: The certificate chain failed OpenSSL’s verification (0:10:CERT_HAS_EXPIRED).
ERROR Defect: OPENSSL_VERIFY: The certificate chain failed OpenSSL’s verification (1:10:CERT_HAS_EXPIRED).
ERROR Defect: OPENSSL_VERIFY: The certificate chain failed OpenSSL’s verification (2:10:CERT_HAS_EXPIRED).
ERROR Defect: OPENSSL_VERIFY: The certificate chain failed OpenSSL’s verification (3:10:CERT_HAS_EXPIRED).
Manually reinstalling the certificates as suggested does get things working again, but not an ideal fix when there's 70+ accounts to deal with