Are there Drupal modules that help process e-mails dynamically
Inmail is designed to be the low level framework to receive mails within Drupal. We proposed in D8 to also implement Mailhandler on top of Inmail and there's good chance this will happen to reduce complexity.

Inmail "works" and you can write plugins to handle the mails.

What you need is a system that supports dynamic mail addresses (through e.g. address expansion). They then need to be redirected / forwarded to the site. This is more a mail server (MTA) configuration than inmail on its own. Through this, every reply is sent to a unique mail address (defined when sending). You can then while handling the mail easily lookup the reference / know the origin.

We plan to add more support for common mail configuration to consider these dynamic situations through configuration only at some point.

Check the issue queue, open feature requests if you can't find a proper issue and start contributing to it! ;-)