I'm not sure if this could cause issues, but maybe you don't need to launch Infopath from the template and thus making a new form.
Instead, save out some already opened and saved forms from the template, but fill in the html path in one of the fields different for each one.
Then when the user uses your link in the flow chart there is a commandline option you can use to open a 'new' form from the template, but using thr merged data from one of the previously created forms (check out /aggregate commandline switch)
One idea for you :-)
Hope this helps.