Usually exim4.conf.template is not overwritten by HestiaCP updates. I have around a 20 HestiaCP servers with the exim4.conf.template file modified, and none of them have ever had any problem with it during all these years.
Also, if you want to be sure, just in case HestiaCP records changes (I doubt it in this case), you can edit it via the “Server Settings” icon (a gear icon on the top right under the admin user) and then edit the “Exim4” service, where you will be editing exim4.conf.template via the HestiaCP panel.
I’m asking because Hestia doesn’t replace the exim4.conf.template completely but it could replace specific directives.
For example, recently we modified the deny message for dns block lists to:
deny message = Rejected because $sender_host_address is in a black list at ${if match{$dnslist_domain}{^[^.]+[.](.+dq[.]spamhaus.*)}{$1}{$dnslist_domain}}\n$dnslist_text
And in a next release we will also modify the dkim_selector directive.