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If you are done using a file, close it.

You should close the files that your were reading and writing when done with that step.

When you get errors, please copy and paste here the FULL contents of the console showing what you entered and the error message.

After looking at your code:
My suggestion was to
First read in...

One approach would be to write the text to a new file and then rename the old file and then the new file. Say add .new to the name of the original file, write the new text to it then rename the...

Look at using some of the String class methods, like substring.