The WHM Copy Account functionality does not remove any data from the source server upon copying the account. If an account was removed from the source server, this alludes to the fact that someone/something initiated a termination of the account that was entirely separate and unrelated to the copy account you processed. The two actions are simply unrelated unless you've heavily customized your server with script hooks that perform such actions.
You may be able to gather further details on who/what terminated the account via:
That will show you all requests made through WHM to terminate an account. At the very least, you should get the IP address of whom initiated the termination. However, if the account was terminated through other means (like manually running /scripts/killacct via shell) it will not show in that log. But, /root/.bash_history may help you there to verify if that's the case.
grep "GET /scripts/killacct?domain" /usr/local/cpanel/logs/access_log
You could always open a ticket with cPanel Support (see my signature for links) and have them perform a cursory look.