Make MSDeploy (Visual Studio) not delete App_Data folder but delete everything else

It can be done when you invoke msdeploy manually – just add the following parameter:

-skip:Directory=\\App_Data

See Web Deploy Operation Settings. The path is a regular expression, so it is quite flexible.

If you deploy using the VS-generated ProjectName.deploy.cmd script, you can also pass this parameter in the _MsDeployAdditionalFlags environment variable (when running that script).

This is the best I’ve come up with for our needs (we have a similar situation as you). I haven’t tried integrating it with VS’s Publish button, since we deploy from command line.

EDIT:

I have learned a few things about MSDeploy since I posted this answer, so I thought I’d update it now.

First of all, the above skip rule skips any operations on the matching path (App_Data). If more granular control is needed, a more verbose syntax is available. For example, to skip only deletes (to keep any extra files on target server, but add any new ones and update existing ones):

-skip:skipaction='Delete',objectname="filePath",absolutepath="\\App_Data\\.*" -skip:skipaction='Delete',objectname="dirPath",absolutepath="\\App_Data\\.*"

This skips deletes of all files and all subfolders (with all their content) in App_Data, but doesn’t prevent adds and updates.

Another useful thing is that skip rules can be defined in the project file (.csproj) so that they are automatically included in the .deploy.cmd script generated along with the package. This makes it unnecessary to pass them to the script through _MsDeployAdditionalFlags.

The above skip rule will be added if the following is included in csproj file:

<PropertyGroup>
  <OnBeforePackageUsingManifest>AddCustomSkipRules</OnBeforePackageUsingManifest>
</PropertyGroup>
<Target Name="AddCustomSkipRules">
  <ItemGroup>
    <MsDeploySkipRules Include="SkipDeleteAppData">
      <SkipAction>Delete</SkipAction>
      <ObjectName>filePath</ObjectName>
      <AbsolutePath>$(_Escaped_PackageTempDir)\\App_Data\\.*</AbsolutePath>
      <XPath>
      </XPath>
    </MsDeploySkipRules>
    <MsDeploySkipRules Include="SkipDeleteAppData">
      <SkipAction>Delete</SkipAction>
      <ObjectName>dirPath</ObjectName>
      <AbsolutePath>$(_Escaped_PackageTempDir)\\App_Data\\.*</AbsolutePath>
      <XPath>
      </XPath>
    </MsDeploySkipRules>
  </ItemGroup>
</Target>

(the names AddCustomSkipRules and SkipDeleteAppData are completely arbitrary; $(_Escaped_PackageTempDir) is supposed to be possibly needed, but in practice I’ve always seen it evaluate to an empty string)

See Web Deploy: Customizing a deployment package and How to set MSDeploy settings in .csproj file for more info.

One caveat: this only adds those rules to the .deploy.cmd script, so it is useless if you want to use the graphical IIS Manager for package deployment, as it doesn’t use that script (the same probably goes for deployment from VS, but I haven’t checked).