If you haven't tried restarting your server yet, that should be the first thing to try. Sometimes if you are doing database changes while the server is running, it will mess something up and inventory will be empty sometimes when you zone and come back sometimes when you zone again. The only way to fix that is restarting the server.
To backup your characters, you can do that easily by using navicat. Install it and connect to your database, then hold down CTRL and click on all of the tables you want to keep and right click them once they are highlighted. For character, you at least want to keep the character_ and inventory tables, but there are probably others that you would want as well. Then, select to dump them to SQL and set a file name to save it to. Once the dump is complete, you should be all set. You can also backup your entire database that way so you can restore it at any time in case anything goes wrong (and it is a good idea to do regular backups). Then, when you want your tables back after you update your database from a fresh install, you can just run the sql file you created. You can do it the same way you run the database setup from the guide or you can just use Navicat and right click the database and select to run a batch file and chose the file you created and run it.
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