Edit: It turns out you are right: the skip directive is ignored when executed from Visual Studio.
Fortunately, there’s a workaround.
What you want is this:
<!-- Skip the deletion of any file within the ErrorLog directory -->
<MsDeploySkipRules Include="SkipErrorLogFolder1">
<SkipAction>Delete</SkipAction>
<ObjectName>filePath</ObjectName>
<AbsolutePath>ErrorLog</AbsolutePath>
</MsDeploySkipRules>
In addition, you need to prevent VS from using the UI-task (which appears to contain a bug regarding the skip rules). You can do this by declaring the following in your wpp.targets or pubxml:
<PropertyGroup>
<UseMsDeployExe>true</UseMsDeployExe>
</PropertyGroup>
I’ve tested this locally and I can confirm that it works as desired: the additional file is updated but no files in the directory are deleted.