diff --git a/NuGet.config b/NuGet.config
index 4c4616c6a576..104875e9392b 100644
--- a/NuGet.config
+++ b/NuGet.config
@@ -18,15 +18,8 @@
     <add key="darc-int-dotnet-aspnetcore-31d685b-2" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-aspnetcore-31d685b2-2/nuget/v3/index.json" />
     <add key="darc-int-dotnet-aspnetcore-31d685b-1" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-aspnetcore-31d685b2-1/nuget/v3/index.json" />
     <!--  End: Package sources from dotnet-aspnetcore -->
-    <!--  Begin: Package sources from dotnet-emsdk -->
-    <!--  End: Package sources from dotnet-emsdk -->
     <!--  Begin: Package sources from dotnet-windowsdesktop -->
     <add key="darc-int-dotnet-windowsdesktop-0dad47b" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-windowsdesktop-0dad47b4/nuget/v3/index.json" />
-    <add key="darc-int-dotnet-windowsdesktop-0dad47b-3" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-windowsdesktop-0dad47b4-3/nuget/v3/index.json" />
-    <add key="darc-int-dotnet-windowsdesktop-0dad47b-2" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-windowsdesktop-0dad47b4-2/nuget/v3/index.json" />
-    <add key="darc-int-dotnet-windowsdesktop-0dad47b-1" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-windowsdesktop-0dad47b4-1/nuget/v3/index.json" />
-    <!--  End: Package sources from dotnet-emsdk -->
-    <!--  Begin: Package sources from dotnet-windowsdesktop -->
     <!--  End: Package sources from dotnet-windowsdesktop -->
     <!--  Begin: Package sources from DotNet-msbuild-Trusted -->
     <!--  End: Package sources from DotNet-msbuild-Trusted -->
@@ -34,8 +27,6 @@
     <add key="darc-int-dotnet-runtime-89ef51c" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-runtime-89ef51c5/nuget/v3/index.json" />
     <add key="darc-int-dotnet-runtime-89ef51c-3" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-runtime-89ef51c5-3/nuget/v3/index.json" />
     <!--  End: Package sources from dotnet-runtime -->
-    <!--  Begin: Package sources from dotnet-windowsdesktop -->
-    <!--  End: Package sources from dotnet-windowsdesktop -->
     <!--  Begin: Package sources from dotnet-sdk -->
     <add key="darc-int-dotnet-sdk-55a73a0" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-sdk-55a73a0e/nuget/v3/index.json" />
     <add key="darc-int-dotnet-sdk-55a73a0-7" value="https://pkgs.dev.azure.com/dnceng/internal/_packaging/darc-int-dotnet-sdk-55a73a0e-7/nuget/v3/index.json" />
@@ -71,6 +62,7 @@
     <!--  Begin: Package sources from dotnet-runtime -->
     <add key="darc-int-dotnet-runtime-89ef51c-3" value="true" />
     <add key="darc-int-dotnet-runtime-89ef51c" value="true" />
+    <!--  End: Package sources from dotnet-runtime -->
     <!--  Begin: Package sources from dotnet-sdk -->
     <add key="darc-int-dotnet-sdk-55a73a0-1" value="true" />
     <add key="darc-int-dotnet-sdk-55a73a0-2" value="true" />
@@ -87,7 +79,6 @@
     <add key="darc-int-dotnet-windowsdesktop-0dad47b-3" value="true" />
     <add key="darc-int-dotnet-windowsdesktop-0dad47b" value="true" />
     <!--  End: Package sources from dotnet-windowsdesktop -->
-    <!--  End: Package sources from dotnet-runtime -->
     <!--End: Package sources managed by Dependency Flow automation. Do not edit the sources above.-->
   </disabledPackageSources>
 </configuration>
diff --git a/eng/pipelines/templates/variables/vmr-build.yml b/eng/pipelines/templates/variables/vmr-build.yml
index fc2aeadb3999..b06695d9b260 100644
--- a/eng/pipelines/templates/variables/vmr-build.yml
+++ b/eng/pipelines/templates/variables/vmr-build.yml
@@ -6,7 +6,7 @@ variables:
 - name: centOSStreamContainer
   value: mcr.microsoft.com/dotnet-buildtools/prereqs:centos-stream9
 - name: fedoraContainer
-  value: mcr.microsoft.com/dotnet-buildtools/prereqs:fedora-40
+  value: mcr.microsoft.com/dotnet-buildtools/prereqs:fedora-41
 - name: ubuntuContainer
   value: mcr.microsoft.com/dotnet-buildtools/prereqs:ubuntu-22.04
 - name: ubuntuArmContainer
@@ -19,7 +19,7 @@ variables:
 - name: centOSStreamName
   value: CentOSStream9
 - name: fedoraName
-  value: Fedora40
+  value: Fedora41
 - name: ubuntuName
   value: Ubuntu2204
 
@@ -30,7 +30,7 @@ variables:
 - name: centOSStreamX64Rid
   value: centos.9-x64
 - name: fedoraX64Rid
-  value: fedora.40-x64
+  value: fedora.41-x64
 - name: ubuntux64Rid
   value: ubuntu.22.04-x64
 - name: ubuntuArm64Rid
diff --git a/src/SourceBuild/content/test/Microsoft.DotNet.SourceBuild.SmokeTests/OmniSharpTests.cs b/src/SourceBuild/content/test/Microsoft.DotNet.SourceBuild.SmokeTests/OmniSharpTests.cs
index a16be098b0b2..ff57040c5b37 100644
--- a/src/SourceBuild/content/test/Microsoft.DotNet.SourceBuild.SmokeTests/OmniSharpTests.cs
+++ b/src/SourceBuild/content/test/Microsoft.DotNet.SourceBuild.SmokeTests/OmniSharpTests.cs
@@ -19,7 +19,7 @@ namespace Microsoft.DotNet.SourceBuild.SmokeTests;
 public class OmniSharpTests : SdkTests
 {
     // Update version as new releases become available: https://github.com/OmniSharp/omnisharp-roslyn/releases
-    private const string OmniSharpReleaseVersion = "1.39.12";
+    private const string OmniSharpReleaseVersion = "1.39.13";
 
     private string OmniSharpDirectory { get; } = Path.Combine(Directory.GetCurrentDirectory(), nameof(OmniSharpTests));