Some orphans can be difficult to delete.
But the link to it is odd; normally that makes it NOT an orphan.
I would look for 2 things. Select the timeline "Sequence July." What is the end action? Is it Flash Menu?
Then in the timeline panel, select that timeline, and select chapter one. Make sure its end action (in the properties panel) is "not set."
You should not have changed your first play. You do want that to be the main menu 1, right?
When you say "extra Flash Menu," it is linked from the Getting Ready button from flash menu page ), right?
Sorry, in my read of your first post, I saw "orphan" and "flash menu" and the flash menu off to the right and did not notice that flash menu is your multipage. The check project error you get is still very odd.
Odd results occur sometimes when a first play menu has an end action of itself rather than "stop." (Your "main menu 1" is set to itself rather than stop.) But I think that has nothing to do with the orphan report.
Often, phantom orphans result from adding something, then changing it, and Encore gets confused. But that generally is not the issue when you restart the project.
Do you mean for the end action of the flash menu to be main menu 1? Does the flash menu time out and you want it to go back?
I would look at the multipage menu in photoshop to see if something is amiss.
But since all is okay except for the check project report, I might just see if it builds, burns, and works okay.