Retain changes to existing files when publishing - tfs

Question

I'm stuck in a scenario where my published file is initially correct, but then later is replaced by it's original version. I suspect that the order of events is wrong, coupled with what's in the root directory.
Essentially I have successfully setup my publishing environment where it executes a custom command to create some JavaScript (which gets created outside of my project). Because a file in source control needs to reference this newly created JavaScript, I am simply copying the file (MyControl.ascx) to a temp location (thus it loses the read lock by TFS) and I am having the custom command update the references to the JS. Once this is done, I gather all the files (custom JavaScript, as well as edited MyControl.ascx in it's temp location) and publish.
It publishes everything first, so I see the new JS as well as the updated MyControl.ascx, but a few minutes later it finishes the publish, and Control looks like how it looked in the root directory.
I think what's happening is it's just pushing out what's in the root (which includes MyControl.ascx) on top of my custom Control (which is in another directory).
<PropertyGroup>
<PipelineCollectFilesPhaseDependsOn>
CustomCollectFiles;
$(PipelineCollectFilesPhaseDependsOn);
</PipelineCollectFilesPhaseDependsOn>
</PropertyGroup>
<Target Name="CustomCollectFiles">
Exec Command="MyCommand.bat"
<ItemGroup>
<_BundledJS Include="$(MSBuildThisFileDirectory)..\..\Includes\javascript\*.js" />
<FilesForPackagingFromProject Include="%(_BundledJS.Identity)">
<DestinationRelativePath>Includes\javascript\%(Filename)%(Extension)
</DestinationRelativePath>
</FilesForPackagingFromProject>
</ItemGroup>
<ItemGroup>
<_UpdatedControl Include="$(MSBuildThisFileDirectory)..\..\TempArea\MyControl.ascx" />
<FilesForPackagingFromProject Include="%(_UpdatedControl.Identity)">
<DestinationRelativePath>Controls\%(Filename)%(Extension)
</DestinationRelativePath>
</FilesForPackagingFromProject>
</ItemGroup>
</Target>
So you can see above i'm taking something that's in ....\TempArea\MyControl.ascx and pushing it out to Controls\%(Filename)%(Extension).
Any ideas how I can tell it to essentially retain my ....\TempArea\MyControl.ascx without then overwriting it with the original MyControl.ascx within the project (....\Controls\MyControl.ascx) ?
Thanks so much!

Answer 1

So I actually ended up figuring it out, and wanted to share:
<ItemGroup>
<_UpdatedControl Include="$(MSBuildThisFileDirectory)..\..\TempArea\MyControl.ascx" />
<FilesForPackagingFromProject Remove="Controls\MyControl.ascx" ></FilesForPackagingFromProject>
<FilesForPackagingFromProject Include="%(_UpdatedControl.Identity)" >
<DestinationRelativePath>Controls\%(RecursiveDir)%(Filename)%(Extension) </DestinationRelativePath>
</FilesForPackagingFromProject>
</ItemGroup>
So you can see here it actually removes the original control, then adds it back.
I also changed the target as such:
<PropertyGroup>
<OnAfterPipelineCollectFilesPhase>
CustomCollectFiles;
$(OnAfterPipelineCollectFilesPhase);
</OnAfterPipelineCollectFilesPhase>
</PropertyGroup>
Let me know if any questions would be happy to help!