Yes, the SmarterMail installer overwrites the \SmarterMail\MRS\web.config on every upgrade.
This will no longer be an issue in v16 going forward as there will be a toggle setting in SmarterMail to force HTTPS.
For those on v15 and older here is the solution:
If you don't want to keep adding your URL Rewrite for HTTP > HTTPS to the \MRS\web.config on every update then you would want to add your URL Rewrite at the Server level instead of the Website level (this is assuming that your server is only running SmarterMail and no other websites).
The global file is located at: %WINDOWS%\system32\inetsrv\config\applicationHost.config
You would add your Rewrite Rule as follows:
<rewrite>
<globalRules>
<rule name="Redirect to HTTPS" stopProcessing="true">
<match url="(.*)" />
<conditions>
<add input="{HTTPS}" pattern="^OFF$" />
</conditions>
<action type="Redirect" url="https://{HTTP_HOST}/{R:1}" redirectType="SeeOther" />
</rule>
</globalRules>
</rewrite>
Of course, you will have to stop the World Wide Web Publishing Service before making this change and restart it when your change is complete, but you do not have to stop/start the SmarterMail service.
Note: if you are hosting multiple sites (i.e., mail.customerdomain.com) but only one SSL Certificate for the Mail Server's Hostname then you'd change
https://{HTTP_HOST}/{R:1} to
https://fqdn.yourserver.com/{R:1}