diff --git a/src/mono/wasm/Wasm.Build.Tests/ProjectProviderBase.cs b/src/mono/wasm/Wasm.Build.Tests/ProjectProviderBase.cs
index 301661f69af9f3..ccd4b435dc5253 100644
--- a/src/mono/wasm/Wasm.Build.Tests/ProjectProviderBase.cs
+++ b/src/mono/wasm/Wasm.Build.Tests/ProjectProviderBase.cs
@@ -129,9 +129,19 @@ public IReadOnlyDictionary<string, DotNetFileName> FindAndAssertDotnetFiles(
                         if (!match.Success)
                             return true;
 
-                        actual[expectedFilename] = new(ExpectedFilename: expectedFilename,
-                                                       Hash: match.Groups[1].Value,
-                                                       ActualPath: actualFile);
+                        // Multiple fingerprinted variants of the same logical file can coexist when
+                        // republishing into an existing output directory: the previous publish's
+                        // fingerprinted copy is not removed, and a rebuild that changes the file's
+                        // content produces a new fingerprint alongside the stale one. Keep the newest
+                        // file so the assertion compares against the current (re)build output instead
+                        // of picking a stale artifact by filename ordering.
+                        if (!actual.TryGetValue(expectedFilename, out DotNetFileName? existingMatch) ||
+                            File.GetLastWriteTimeUtc(actualFile) >= File.GetLastWriteTimeUtc(existingMatch.ActualPath))
+                        {
+                            actual[expectedFilename] = new(ExpectedFilename: expectedFilename,
+                                                           Hash: match.Groups[1].Value,
+                                                           ActualPath: actualFile);
+                        }
                     }
                     else
                     {
diff --git a/src/mono/wasm/testassets/EntryPoints/NativeRebuildNewAssembly.cs b/src/mono/wasm/testassets/EntryPoints/NativeRebuildNewAssembly.cs
index bff7ffb3827a40..931f177dc8a10e 100644
--- a/src/mono/wasm/testassets/EntryPoints/NativeRebuildNewAssembly.cs
+++ b/src/mono/wasm/testassets/EntryPoints/NativeRebuildNewAssembly.cs
@@ -1,6 +1,7 @@
 using System;
 using System.Security.Cryptography;
 using System.Text;
+using System.Text.RegularExpressions;
 public class Test
 {
     public static int Main()
@@ -12,6 +13,13 @@ public static int Main()
             byte[] hashBytes = sha256.ComputeHash(inputBytes);
             Console.WriteLine($"Hash of {input}: {Convert.ToBase64String(hashBytes)}");
         }
+
+        // Also reference System.Text.RegularExpressions, which is not otherwise part of
+        // the test app's closure, so that rebuilding pulls in a *new* assembly. This
+        // ensures native artifacts that depend on the set of assemblies (e.g. the AOT
+        // modules table driver-gen.c) are regenerated on rebuild.
+        bool isMatch = Regex.IsMatch(input, "[A-Za-z]+");
+        Console.WriteLine($"Input '{input}' matches: {isMatch}");
         return 42;
     }
 }