Today you have a flag that tells us if an issue has been deleted.  However, if a project is deleted, we have 2 issues:

• Issues in that project are not flagged as deleted - they are still returned in queries
• There isn't a flag telling us the project has been deleted, so we can't filter it out of the project list.

There is a webhook option for "Project - Deleted" so you may be able to implement this using an equivalent process as the deleted issue process.

Thanks!