Shoes Packager behaviour is sometimes ugly. I think you're using windows, so i'll try to explain what seems to happen:
You have a bundled Shoes-App (a standalone .exe file). Every Time you start it by double clicking, it will extract itself in a new temp dir (located under c:\tmp\tempFileDirectory). So, it is a NEW temporary Directory, everytime!
The current path also is set to this tmp directory, which also includes the txt files you bundled into the app, in it's original state. If you change the content of the files during the app execution, and restart the app, your changes are gone, because in the new created tmp dir, there is a fresh copy of the original txt files. so far, it is a BAD idea to put your data files (txt in your case, or SQLITE-database-files, or config files, ...) into the bundles app.
Better way:
create a "hidden" folder (folder's name should start with an ".") in the user's home folder. On windows it should be something like "c:\Users\YourName". Create there everything you need, this directory won't be temporal, so you can access it everytime without problems. This should general be a better solution when programming desktop stuff, not just while using shoes.