How do I remove a repository from the Projects list?

In the Projects list, remove the entry. The repository stays exactly where it is on disk; Innesta simply stops offering it.

Also removed: its entry from the Dock menu and from the menu bar extra, both of which read the same list, and whatever Innesta had put in Spotlight for it.

Innesta keeps a security-scoped bookmark for repositories outside the folders macOS lets applications read by default. Removing the project releases it, so opening that folder again asks macOS for permission again.