The Jar file is read-only on the device. Your midlet can read the text file, but can not write something back. (This is by design, the jar files may get preinstalled into ROM, or they may be signed. Or the device may do dome optimisations when your midlet is installed.)
You can write information into a thing called RecordStore. If you just need a flag, you write this flag into a RecordStore. The next time your midlet starts, you check if the recordstore exists and contains your flag.