Some more substitution tests. It seems like it's working as it should.

src/test/java/net/minecraftforge/fml/common/registry/RegistryTestSuite.java

@@ -7,7 +7,7 @@ import org.junit.runners.Suite;
  * Run the full suite of tests
  */
 @RunWith(Suite.class)
-@Suite.SuiteClasses({VanillaRegistryTests.class, FreezingTests.class, SubstitutionTests.class})
+@Suite.SuiteClasses({VanillaRegistryTests.class, FreezingTests.class, SubstitutionRemoveRestoreTest.class, SubstitutionInjectionTest.class})
 public class RegistryTestSuite
 {
 }

src/test/java/net/minecraftforge/fml/common/registry/SubstitutionInjectionTest.java

@@ -0,0 +1,76 @@
+package net.minecraftforge.fml.common.registry;
+
+import net.minecraft.block.Block;
+import net.minecraft.block.BlockDirt;
+import net.minecraft.init.Blocks;
+import net.minecraft.init.Bootstrap;
+import net.minecraft.util.ResourceLocation;
+import net.minecraftforge.fml.common.DummyModContainer;
+import net.minecraftforge.fml.common.Loader;
+import net.minecraftforge.fml.common.ModMetadata;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+
+/**
+ * Substitution test harness - tests that substitutions behave correctly
+ */
+@RunWith(ForgeTestRunner.class)
+public class SubstitutionInjectionTest
+{
+    private ResourceLocation myDirt = new ResourceLocation("minecraft:dirt");
+    private BlockDirt toSub = new BlockDirt() {
+
+    };
+
+    @BeforeClass
+    public static void setup()
+    {
+        Loader.instance();
+        Bootstrap.register();
+        Loader.instance().setupTestHarness(new DummyModContainer(new ModMetadata() {{
+            modId = "test";
+        }}));
+    }
+
+    @Test
+    public void testSubstitutionInjection() throws Exception
+    {
+        // Capture snapshot prior to registering the substitution - this is a world state "pre-substitute"
+        final PersistentRegistryManager.GameDataSnapshot snapshot = PersistentRegistryManager.takeSnapshot();
+
+        GameRegistry.addSubstitutionAlias("minecraft:dirt", GameRegistry.Type.BLOCK, toSub);
+        PersistentRegistryManager.freezeData();
+        ObjectHolderRegistry.INSTANCE.applyObjectHolders();
+
+        final FMLControlledNamespacedRegistry<Block> blockRegistry = (FMLControlledNamespacedRegistry<Block>)PersistentRegistryManager.findRegistryByType(Block.class);
+
+        // TEST 1: Does my substitute take effect? The substitute should be found in the registry
+        Block fnd = blockRegistry.getValue(myDirt);
+        Block currDirt = Blocks.DIRT;
+        assertEquals("Got my dirt substitute - Blocks", toSub, currDirt);
+        assertEquals("Got my dirt substitute - Blocks and registry", currDirt, fnd);
+        assertEquals("Got my dirt substitute - registry", toSub, fnd);
+
+        // TEST 2: Does the substitute get injected when told by loading operation? The substitute should be found in the registry
+        PersistentRegistryManager.injectSnapshot(snapshot, true, true);
+        ObjectHolderRegistry.INSTANCE.applyObjectHolders();
+        fnd = blockRegistry.getValue(myDirt);
+        currDirt = Blocks.DIRT;
+        assertEquals("Got my dirt substitute - Blocks", toSub, currDirt);
+        assertEquals("Got my dirt substitute - Blocks and registry", currDirt, fnd);
+        assertEquals("Got my dirt substitute - registry", toSub, fnd);
+
+        // TEST 3: Does the substitute get restored when reverting to frozen state? The substitute should be found in the registry again
+        PersistentRegistryManager.revertToFrozen();
+        ObjectHolderRegistry.INSTANCE.applyObjectHolders();
+        fnd = blockRegistry.getValue(myDirt);
+        currDirt = Blocks.DIRT;
+        assertEquals("Got my dirt substitute - Blocks", toSub, currDirt);
+        assertEquals("Got my dirt substitute - Blocks and registry", currDirt, fnd);
+        assertEquals("Got my dirt substitute - registry", toSub, fnd);
+    }
+}

src/test/java/net/minecraftforge/fml/common/registry/SubstitutionRemoveRestoreTest.java

@@ -19,7 +19,7 @@ import static org.junit.Assert.assertNotEquals;
  * Substitution test harness - tests that substitutions behave correctly
  */
 @RunWith(ForgeTestRunner.class)
-public class SubstitutionTests
+public class SubstitutionRemoveRestoreTest
 {
     private ResourceLocation myDirt = new ResourceLocation("minecraft:dirt");
     private BlockDirt toSub = new BlockDirt() {
@@ -37,7 +37,7 @@ public class SubstitutionTests
     }
 
     @Test
-    public void testSubstitution() throws Exception
+    public void testSubstitutionRemovalAndRestore() throws Exception
     {
         GameRegistry.addSubstitutionAlias("minecraft:dirt", GameRegistry.Type.BLOCK, toSub);
         PersistentRegistryManager.freezeData();