Clear after saving, save before clearing.

src/main/java/com/gmail/nossr50/commands/database/MmoupdateCommand.java

@@ -23,6 +23,7 @@ public class MmoupdateCommand implements CommandExecutor {
         switch (args.length) {
             case 0:
                 sender.sendMessage(LocaleLoader.getString("Commands.mmoupdate.Start"));
+                UserManager.saveAll();
                 UserManager.clearAll();
                 convertToMySQL();
 

src/main/java/com/gmail/nossr50/mcMMO.java

@@ -168,7 +168,8 @@ public class mcMMO extends JavaPlugin {
         try {
             reloadDisableHelper();      // Prevent Berserk from getting "stuck"
             UserManager.saveAll();      // Make sure to save player information if the server shuts down
-            PartyManager.saveParties();
+            UserManager.clearAll();     // Should always clear after saving
+            PartyManager.saveParties(); // Save our parties
             placeStore.saveAll();       // Save our metadata
             placeStore.cleanUp();       // Cleanup empty metadata stores
         }