Hi list,
don't know if this can be useful. 
I developed a perl wrapper to allow OTRS to handle multiple Ticket numbers in Subject.
I wrote a blog post with all details and now is working on my company server since some day with no issues.

Here the blog post
 https://scubarda.wordpress.com/2016/07/29/configure-otrs-to-process-multiple-tickets-in-email-subject/

Ciao
Giovanni