diff --git a/scripts/buildsystems/msbuild/vcpkg.targets b/scripts/buildsystems/msbuild/vcpkg.targets
index 7fb9ad7447..4258a352a7 100644
--- a/scripts/buildsystems/msbuild/vcpkg.targets
+++ b/scripts/buildsystems/msbuild/vcpkg.targets
@@ -269,6 +269,14 @@
     <Message Text="@(VcpkgAppLocalDLLs,'%0A')" Importance="Normal" Condition="$(_ZVcpkgAppLocalExitCode) == 0" />
     <ItemGroup Condition="$(_ZVcpkgAppLocalExitCode) == 0">
       <ReferenceCopyLocalPaths Include="@(VcpkgAppLocalDLLs)" />
+      <!-- Register the deployed DLLs as file writes so MSBuild's IncrementalClean
+           doesn't treat them as orphan outputs and delete them. Without this, any
+           clean-file entries recorded by AppLocalFromInstalledPreserve on a previous
+           link-skipped build cause IncrementalClean to delete the DLLs on the next
+           build where the link runs, immediately after they were deployed. The paths
+           are re-based to $(OutDir) because z-applocal logs source paths while
+           applocal.ps1 logs destination paths. -->
+      <FileWrites Include="@(VcpkgAppLocalDLLs -> '$(OutDir)%(Filename)%(Extension)')" />
     </ItemGroup>
   </Target>