My recommendation is not use cPanel migrate function if you wish to have working Letsencrypt on those accounts.
You are better off manually transferring cPanel accounts. The migration function works but I would consider it beta at best. Trying to get any help or advice cost, which is fine but seems like admin would want the function working...
Only thing I can get out of support is:
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the issue related to redirection. We will be happy to assist you but unfortunately you don't have an active support service or your support service has expired.
For more detailed check of your server and services configuration issues you can check our Support services.
Each configuration changes or issue which requires free time for resolving will need to be done via our Support services.
Support orders are usually approved within 24 hours, once the order is approved you will be able to use our support tickets.
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I manually added cpanel account by simply decompressing into site public_html folder. Then setup mySQL, imported database via phpmyadmin. Had to of course fix permissions and site working fine. Then installed letsencrypt without any issues at all. Just do not use the migration function, it causes issues.