Assuming you are running desktop Monarch, and aren't drowning in the quicksand of the Digital Object Repository in Automator, then deleting a project is simple. Open Windows Explorer, browse to the relevant folder, delete the xprj or dprj file in question.
The project contains three bits of information: what report(s) to open, what model to apply, and what export(s) to perform. That's it. Deleting the project is perfectly safe - the reports and models and any exports you have run already won't be affected.