Currently, as of Jira 7.12.3, the following scenario occurs:

1. Create a mail handler that creates Issues of Issue Type X in a specific project, as in:
   • "Create a new issue or add a comment to an existing issue"
   • "Create a new issue from each email message"
2. Remove issue type X from the project's issue type scheme

Expected result:
The creation of issues from the mail handler will fail due to the issue type being invalid.

Actual result:
The issue is created as issue type X

The suggestion is to either reject these emails when the mail handler is configured to use an issue type that is not included in the project's Issue Type scheme OR to prevent an Issue Type being removed from an Issue Type scheme if there is a mail handler configured to use that Issue type for a project that has that Issue Type scheme linked.