The layout is remembering a bad or old version of the resource that you don’t have.
Open that layout and delete the resource that is being complained about.
Load the new resource and set your layout just the way you want it.
Save the Layout WITH A NEW NAME.
Close Paratext and Open it. Close all the windows.
Open the layout with the new name.
It should open without a message and look the way you want it.
Delete the old layout.
If you wish, you could save the new layout with the old name, but I’d probably reboot first to wipe Paratext’s memory of the old layout. That may be overdoing it, but …
You will need to do the same thing for any Text Collections as well.
Blessings,