O seguinte é o meu arquivo CustomProfile.pubxml que eu uso para deixar minha pasta conhecida pelo LetsEncrypt, assim como outras pastas sozinhas. Adicione os itens abaixo em negrito para excluir arquivos de processamento no servidor, como conteúdo gerado pelo usuário. Isso só foi testado no Visual Studio 2017, com o Server 2016.
<?xml version="1.0" encoding="utf-8"?>
<!--
This file is used by the publish/package process of your Web project.
You can customize the behavior of this process by editing this MSBuild file.
In order to learn more about this please visit
https://go.microsoft.com/fwlink/?LinkID=208121.
-->
<Project ToolsVersion="4.0" xmlns="http://schemas.microsoft.com/developermsbuild/2003">
<PropertyGroup>
<WebPublishMethod>MSDeploy</WebPublishMethod>
</PropertyGroup>
<PropertyGroup>
<LastUsedBuildConfiguration>Release</LastUsedBuildConfiguration>
<LastUsedPlatform>Any CPU</LastUsedPlatform>
<SiteUrlToLaunchAfterPublish>https://www.vinceworks.com</SiteUrlToLaunchAfterPublish>
<LaunchSiteAfterPublish>True</LaunchSiteAfterPublish>
<ExcludeApp_Data>True</ExcludeApp_Data>
<MSDeployServiceURL>https://www.vinceworks.com</MSDeployServiceURL>
<DeployIisAppPath>VinceWorks</DeployIisAppPath>
<RemoteSitePhysicalPath />
<SkipExtraFilesOnServer>False</SkipExtraFilesOnServer>
<MSDeployPublishMethod>WMSVC</MSDeployPublishMethod>
<EnableMSDeployBackup>True</EnableMSDeployBackup>
<UserName>Vince</UserName>
<_SavePWD>True</_SavePWD>
<PrecompileBeforePublish>True</PrecompileBeforePublish>
<EnableUpdateable>True</EnableUpdateable>
<DebugSymbols>False</DebugSymbols>
<WDPMergeOption>DonotMerge</WDPMergeOption>
</PropertyGroup>
<ItemGroup>
<MsDeploySkipRules Include="CustomSkipFolder">
<ObjectName>dirPath</ObjectName>
<AbsolutePath>VinceWorks\\.well-known</AbsolutePath><!--Regular Expression here-->
</MsDeploySkipRules>
</ItemGroup>
<ItemGroup>
<MsDeploySkipRules Include="CustomSkipFolder">
<ObjectName>dirPath</ObjectName>
<AbsolutePath>VinceWorks\Media</AbsolutePath>
</MsDeploySkipRules>
</ItemGroup>
<ItemGroup>
<MsDeploySkipRules Include="CustomSkipFolder">
<ObjectName>dirPath</ObjectName>
<AbsolutePath>\Views</AbsolutePath>
</MsDeploySkipRules>
</ItemGroup>
</Project>