diff --git a/rpgregions/src/main/java/net/islandearth/rpgregions/commands/RPGRegionsCommand.java b/rpgregions/src/main/java/net/islandearth/rpgregions/commands/RPGRegionsCommand.java
index c3c7af2..789f498 100644
--- a/rpgregions/src/main/java/net/islandearth/rpgregions/commands/RPGRegionsCommand.java
+++ b/rpgregions/src/main/java/net/islandearth/rpgregions/commands/RPGRegionsCommand.java
@@ -82,7 +82,11 @@ public class RPGRegionsCommand extends BaseCommand {
 	@CommandCompletion("@regions")
 	public void onRemove(CommandSender sender, ConfiguredRegion configuredRegion) {
 		if (configuredRegion != null) {
-			configuredRegion.delete(plugin);
+			try {
+				configuredRegion.delete(plugin);
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
 			plugin.getManagers().getRegionsCache().removeConfiguredRegion(configuredRegion.getId());
 			sender.sendMessage(StringUtils.colour("&cRemoved configured region " + configuredRegion.getId() + "!"));
 		} else {
diff --git a/rpgregions/src/main/java/net/islandearth/rpgregions/managers/RPGRegionsManagers.java b/rpgregions/src/main/java/net/islandearth/rpgregions/managers/RPGRegionsManagers.java
index bd90e41..3e0d8fd 100644
--- a/rpgregions/src/main/java/net/islandearth/rpgregions/managers/RPGRegionsManagers.java
+++ b/rpgregions/src/main/java/net/islandearth/rpgregions/managers/RPGRegionsManagers.java
@@ -34,11 +34,14 @@ import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.Reader;
+import java.nio.file.Files;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 import java.util.logging.Level;
+import java.util.stream.Collectors;
 
 public class RPGRegionsManagers {
 
@@ -99,20 +102,33 @@ public class RPGRegionsManagers {
 			e.printStackTrace();
 		}
 
-		for (File file : folder.listFiles()) {
-			// Exclude non-json files
-			if (file.getName().endsWith(".json")) {
-				try {
-					Reader reader = new FileReader(file);
-					ConfiguredRegion region = plugin.getGson().fromJson(reader, ConfiguredRegion.class);
-					if (!region.getId().equals("exampleconfig")) regionsCache.addConfiguredRegion(region);
-					if (region.getRequirements() != null) region.getRequirements().forEach(regionRequirement -> plugin.getLogger().warning("Warning: Region " + region.getId() + " uses requirements. These are highly experimental and there may be bypasses."));
-					reader.close();
-				} catch (Exception e) {
-					plugin.getLogger().severe("Error loading region config " + file.getName() + ":");
-					e.printStackTrace();
-				}
-			}
+		try {
+			Files.walk(Paths.get(folder.getPath()))
+					.filter(Files::isRegularFile)
+					.collect(Collectors.toList())
+					.forEach(path -> {
+						File file = path.toFile();
+						if (regionsCache.getConfiguredRegions().containsKey(file.getName().replace(".json", ""))) {
+							plugin.getLogger().severe("Duplicate region files have been found for " + file.getName() + ". " +
+									"In order to protect your data, the plugin will NOT load the duplicate region config.");
+							return;
+						}
+						// Exclude non-json files
+						if (file.getName().endsWith(".json")) {
+							try {
+								Reader reader = new FileReader(file);
+								ConfiguredRegion region = plugin.getGson().fromJson(reader, ConfiguredRegion.class);
+								if (!region.getId().equals("exampleconfig")) regionsCache.addConfiguredRegion(region);
+								if (region.getRequirements() != null) region.getRequirements().forEach(regionRequirement -> plugin.getLogger().warning("Warning: Region " + region.getId() + " uses requirements. These are highly experimental and there may be bypasses."));
+								reader.close();
+							} catch (Exception e) {
+								plugin.getLogger().severe("Error loading region config " + file.getName() + ":");
+								e.printStackTrace();
+							}
+						}
+					});
+		} catch (IOException e) {
+			e.printStackTrace();
 		}
 
 		this.regenerationManager = new RegenerationManager(plugin);
diff --git a/rpgregions/src/main/java/net/islandearth/rpgregions/managers/data/region/ConfiguredRegion.java b/rpgregions/src/main/java/net/islandearth/rpgregions/managers/data/region/ConfiguredRegion.java
index 0d5e661..e8eb38f 100644
--- a/rpgregions/src/main/java/net/islandearth/rpgregions/managers/data/region/ConfiguredRegion.java
+++ b/rpgregions/src/main/java/net/islandearth/rpgregions/managers/data/region/ConfiguredRegion.java
@@ -27,10 +27,14 @@ import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
 import java.io.Writer;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.UUID;
+import java.util.stream.Collectors;
 
 public class ConfiguredRegion {
 
@@ -298,7 +302,8 @@ public class ConfiguredRegion {
 	}
 
 	public void save(RPGRegions plugin) throws IOException {
-		File file = new File(plugin.getDataFolder() + "/regions/" + this.id + ".json");
+		File file = this.findFile(plugin);
+		if (file == null) file = new File(plugin.getDataFolder() + "/regions/" + this.id + ".json");
 		Writer writer = new FileWriter(file);
 		Gson gson = plugin.getGson();
 		gson.toJson(this, writer);
@@ -306,8 +311,29 @@ public class ConfiguredRegion {
 		writer.close();
 	}
 
-	public void delete(RPGRegions plugin) {
-		File file = new File(plugin.getDataFolder() + "/regions/" + this.id + ".json");
-		file.delete();
+	public boolean delete(RPGRegions plugin) throws IOException {
+		File file = this.findFile(plugin);
+		if (file == null) file = new File(plugin.getDataFolder() + "/regions/" + this.id + ".json");
+		return file.delete();
+	}
+
+	@Nullable
+	private File findFile(RPGRegions plugin) throws IOException {
+		File folder = new File(plugin.getDataFolder() + "/regions/");
+		List<Path> valid = Files.walk(Paths.get(folder.getPath()))
+				.filter(path -> Files.isRegularFile(path) && path.toFile().getName().equals(this.id + ".json"))
+				.collect(Collectors.toList());
+		if (valid.isEmpty()) return null;
+		if (valid.size() > 1) {
+			plugin.getLogger().severe("Duplicate region files have been found for " + this.id + ". " +
+					"In order to protect your data, the plugin will NOT save the region config.");
+			throw new IOException("Duplicate region file");
+		}
+
+		File file = null;
+		for (Path path : valid) {
+			file = path.toFile();
+		}
+		return file;
 	}
 }