What is the exact code you have been using? It's hard to help you fix something we can't see ...

As for basic issues, you cannot edit a file directly from Perl. You (generally) have to:

1. Open a filehandle to read the file
2. Read the file into some data structure
3. Close the read-only filehandle
4. Edit the data structure
5. Open a filehandle to overwrite the file
6. Write the data structure to the file
7. Close the write-only filehandle

I suspect you're missing the first close and second open. That's a common mistake among newbies. To match the above 7 steps to your needs, you'll need to repeat steps 1-3 for both files.