To easily remove the lines using a shell scirpt you will have to have some sort of delimiter. The problem is if those delimiters appear elsewhere in the source, it makes the issue more complex. For example, based on the current blank line delimiters you can use someting as simple as this:
sed '/^$/,/^$/D' original_file.txt
This will remove everything between and including the blank lines. The problem is if you have other blank lines, it is likely to delete other things as well.
A better route may be to write a perl script that reads the file and removes the lines that match common headers. This too can be an issue if the header text appears elsewhere in the source.