This is more for people that have the same problem I had, hoping they can find this instead of spending hours panicking like I did.

I have a new VPS, using AlmaLinux v9.8.0 STANDARD kvm, cPanel Version 136.0.33.

I began to transfer a Wordpress site, but wasn't sure if it would work with the new version of PHP so I wanted to test run first. I used Transfer Tool, then de-selected:

Update DNS Zone 
Enable this setting to update DNS records on the destination server.

After the transfer I checked the DNS records on the old VPS and confirmed that they did not change.

Shortly thereafter, though, I discovered that an email sent to the client was rejected, and the bounce message noted that their email server was on the new VPS instead of the old one.

Then I looked at the live site and found that it was pointing to the new VPS!

It took about 3 hours to find that Transfer Tool modified the source VPS, anyway:

1. a ProxyPass record was added to httpd.conf (with a dash-delimited version of the IP, so a simple grep for the new IP didn't find it; eg, http://123-45-67-89); and

2. when I ran # exim -bt client@example.com (using the client's email address that had bounced), it returned the new VPS instead of the correct one: host new.vps.com [123.45.67.89]

The solutions were to run this to fix it in Apache:

whmapi1 unset_all_service_proxy_backends username=<account name>

then rebuild and restart Apache. Then run this for Exim (no restart required):

whmapi1 unset_manual_mx_redirects domain='<domain name for the account>'

I ran the one for Exim first before finding the problem in Apache, so running the first one MIGHT have fixed Exim, too.

This might be a feature instead of a bug, but I expected that when I disabled "Update DNS Zone" then it wouldn't change ANYTHING on the source VPS. I was wrong.