You can use eaccmd to modify a script in an application.

To modify an existing script in eaccmd, use the following syntax:

update-script [--force]  --app app_id --script script_id [--cmd command --wd working_dir --log-file log_file] | [--def def_file]

For example:

update-script --app myApp --script newbaseline.pl --def myApp.xml