I've noticed a few of these tickets but I'm not certain how to reproduce so creating this Suggestion as a tracker for now.

Incorrect message appears on team-managed if the project's filter refers to a project with a changed issue key. Error message:
 

Timelines are designed for a single project
To view this project timeline, the project administrator needs to edit your board filter to include issues from Get Started with Next-Gen2 only., (opens new window)
But wait! You have access to Plans, a powerful planning tool that lets you schedule and track work across multiple teams and projects. To create a cross-project plan using Plans, select Create plan from the Plans menu at the top of your screen. Or click below to get started!

Filter in question only refers to a single project:

The problem is not that more than one project is referred to in the query, but rather that the project key has been changed and is therefore no longer accurate.

Notes
I can't reproduce this issue in newly created team-managed Jira Software projects as I don't see the option to view a team-managed project's filter either from within the project or by search on https://YOUR_SITE_NAME.atlassian.net/jira/filters?page=1&selectedGroup=anything&selectedProject=anything&sortKey=name&sortOrder=ASC

On older team-managed Jira Software I do have access to https://YOUR_SITE_NAME.atlassian.net/jira/software/c/projects/<project key</boards/<board id>?config=filter where I can edit the filter, and the filter also appears on the View all filters page.