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depends on what you define as special.

This will escape any non-alphanum,hyphen or underscore:

$ echo 'qwerty123@!,' | sed 's/[^[:alnum:]_-]/\\&/g'
qwerty123\@\!\,

Hi,
Use back slash before $

ant -q -buildfile \$HOME/\$3/build.xml \$4

Hi, use quotes around the first EOF
cat > "$1/$2.sh" << "EOF"
#! /bin/bash
ant -q -buildfile $HOME/$3/build.xml $4
...
EOF

Just run following and test whether shc is creating executables $ shc -v -r -T -f your_shell_script

The code you are feeding into shc. It is obviously relevant.