There is not a HPE document that details out a proper process or standard for this type of action. I will though detail out a solution below that can achieve what you need done, which is the removal of the template script area from the new project.
First, we need to enter site admin and ensure our FTP port parameter is in place. Under the Site Configuration tab, for the listed parameters, check to see if FTP_PORT is present. If not, add it and give it a value of 2121. Typically this port should be free but you might want to check to be sure.
After the ftp port is added or known to exist, next we will want to use it to view the repository for the newly created project. I prefer to use windows explorer to ftp over as in the explorer window its is easy to sort files by date, size, etc.
Here are the steps to create a ftp shortcut in Windows 7. Similar for other versions of Windows.
1. Open Computer by clicking the ''Start'' button, and then clicking Computer.
2. Right-click anywhere in the folder, and then click Add a Network Location.
3. In the wizard, select Choose a custom network location, and then click Next.
4. Enter the name of the FTP site, example being ftp://theadmin@myalmserver:2121/ The user ''theadmin'' is my site admin user, myalmserver is the name of my ALM 11.52 server. Click Next to continue.
5. Enter name for the shortcut. I tend to just name it ALM 11.52 FTP or similar
6. Screen will have created, and gives you option to Open when Finish. Click Finish.
7. FTP shortcut should open and you should be prompted to enter password for the site admin user name you entered. Option below has ''Save Password'' and if you click it, you only need to log in the one time.
Use your new shortcut to find your domain and the newly created project. Open the project and look for the scripts folder. Open that and you will see list of worfklow scripts added. Template scripts will have a name such as **Tempalte_testplan.tds** or similar. You will want to delete any script that has **Template_** in front as those would be your template scripts.
After deletion of all the **Template_** scripts, suggest you then stop and restart the ALM service. This in short would force a reload of the project, a new read from repository. Get service back up, login to project and enter customization. Open the script editor and you should see that the template script section is gone and only the project script section is present. Now you just have the one area for adding in new workflow code. No more conflicts.