diff --git a/src/main/java/io/github/thebusybiscuit/slimefun4/storage/backend/legacy/LegacyStorage.java b/src/main/java/io/github/thebusybiscuit/slimefun4/storage/backend/legacy/LegacyStorage.java
index 5b35e5e4cc..d7981a5466 100644
--- a/src/main/java/io/github/thebusybiscuit/slimefun4/storage/backend/legacy/LegacyStorage.java
+++ b/src/main/java/io/github/thebusybiscuit/slimefun4/storage/backend/legacy/LegacyStorage.java
@@ -85,9 +85,15 @@ public void savePlayerData(@Nonnull UUID uuid, @Nonnull PlayerData data) {
 
         // Save research
         playerFile.setValue("rearches", null);
-        for (Research research : data.getResearches()) {
-            // Legacy data uses IDs
-            playerFile.setValue("researches." + research.getID(), true);
+        for (Research research : Slimefun.getRegistry().getResearches()) {
+            // Save the research if it's researched
+            if (data.getResearches().contains(research)) {
+                playerFile.setValue("researches." + research.getID(), true);
+
+            // Remove the research if it's no longer researched
+            } else if (playerFile.contains("researches." + research.getID())) {
+                playerFile.setValue("researches." + research.getID(), null);
+            }
         }
 
         // Save backpacks
diff --git a/src/test/java/io/github/thebusybiscuit/slimefun4/storage/backend/TestLegacyBackend.java b/src/test/java/io/github/thebusybiscuit/slimefun4/storage/backend/TestLegacyBackend.java
index 804f24306a..1859659999 100644
--- a/src/test/java/io/github/thebusybiscuit/slimefun4/storage/backend/TestLegacyBackend.java
+++ b/src/test/java/io/github/thebusybiscuit/slimefun4/storage/backend/TestLegacyBackend.java
@@ -62,6 +62,7 @@ public static void unload() throws IOException {
         FileUtils.deleteDirectory(new File("data-storage"));
     }
 
+    // Test simple loading and saving of player data
     @Test
     void testLoadingResearches() throws IOException {
         // Create a player file which we can load
@@ -275,6 +276,102 @@ void testSavingWaypoints() throws InterruptedException {
         Assertions.assertEquals("world", waypoint.getLocation().getWorld().getName());
     }
 
+    // Test realistic situations
+    @Test
+    void testResearchChanges() throws InterruptedException {
+        UUID uuid = UUID.randomUUID();
+        File playerFile = new File("data-storage/Slimefun/Players/" + uuid + ".yml");
+
+        OfflinePlayer player = Bukkit.getOfflinePlayer(uuid);
+        PlayerProfile profile = TestUtilities.awaitProfile(player);
+
+        // Unlock all researches
+        for (Research research : Slimefun.getRegistry().getResearches()) {
+            profile.setResearched(research, true);
+        }
+
+        // Save the player data
+        LegacyStorage storage = new LegacyStorage();
+        storage.savePlayerData(uuid, profile.getPlayerData());
+
+        // Assert the file exists and data is correct
+        Assertions.assertTrue(playerFile.exists());
+        PlayerData assertion = storage.loadPlayerData(uuid);
+        Assertions.assertEquals(10, assertion.getResearches().size());
+        for (int i = 0; i < 10; i++) {
+            Assertions.assertTrue(assertion.getResearches().contains(Slimefun.getRegistry().getResearches().get(i)));
+        }
+
+        // Now let's change the data and save it again
+        profile.setResearched(Slimefun.getRegistry().getResearches().get(3), false);
+
+        // Save the player data
+        storage.savePlayerData(uuid, profile.getPlayerData());
+
+        // Assert the file exists and data is correct
+        Assertions.assertTrue(playerFile.exists());
+        System.out.println("update assertion");
+        assertion = storage.loadPlayerData(uuid);
+        Assertions.assertEquals(9, assertion.getResearches().size());
+        for (int i = 0; i < 10; i++) {
+            if (i != 3) {
+                Assertions.assertTrue(assertion.getResearches().contains(Slimefun.getRegistry().getResearches().get(i)));
+            }
+        }
+    }
+
+    // Test realistic situations - when we fix the serialization issue
+    // @Test
+    // void testBackpackChanges() throws InterruptedException {}
+
+    @Test
+    void testWaypointChanges() throws InterruptedException {
+        // Create mock world
+        World world = server.createWorld(WorldCreator.name("world").environment(Environment.NORMAL));
+
+        // Create a player file which we can load
+        UUID uuid = UUID.randomUUID();
+        File playerFile = new File("data-storage/Slimefun/Players/" + uuid + ".yml");
+
+        OfflinePlayer player = Bukkit.getOfflinePlayer(uuid);
+        PlayerProfile profile = TestUtilities.awaitProfile(player);
+
+        profile.addWaypoint(new Waypoint(
+            player.getUniqueId(),
+            "test",
+            new Location(world, 1, 2, 3, 4, 5),
+            ChatColor.GREEN + "Test waypoint"
+        ));
+
+        Waypoint test2 = new Waypoint(
+            player.getUniqueId(),
+            "test2",
+            new Location(world, 10, 20, 30, 40, 50),
+            ChatColor.GREEN + "Test 2 waypoint"
+        );
+        profile.addWaypoint(test2);
+
+        // Save the player data
+        LegacyStorage storage = new LegacyStorage();
+        storage.savePlayerData(uuid, profile.getPlayerData());
+
+        // Assert the file exists and data is correct
+        Assertions.assertTrue(playerFile.exists());
+        PlayerData assertion = storage.loadPlayerData(uuid);
+        Assertions.assertEquals(2, assertion.getWaypoints().size());
+
+        // Remove one
+        profile.removeWaypoint(test2);
+
+        // Save the player data
+        storage.savePlayerData(uuid, profile.getPlayerData());
+
+        // Assert the file exists and data is correct
+        Assertions.assertTrue(playerFile.exists());
+        assertion = storage.loadPlayerData(uuid);
+        Assertions.assertEquals(1, assertion.getWaypoints().size());
+    }
+
     // Utils
     private static void setupResearches() {
         for (int i = 0; i < 10; i++) {