The screenshot in the original post shows resources that say, “External”. This means these resources are from when the setting wasn’t enabled, or before the setting existed.
Changing the setting unfortunately doesn’t doesn’t migrate the existing resources 
– at least that’s what the detail-text below the settings says.
It would be great if there were a way to do that. Maybe a RW Support person knows how? or maybe @tpbradley?
(p.s. if there’s a way to do this – even a complicated terminal command or something – it would really help me when I’m doing support. – thx)
The reason for these broken links is probably related to the Big Sur update (or moving to a new computer, etc.). Big Sur is very strict with the permissions each app has to read random files on your computer. RW gets permission to read the project file itself when you open the project – but that’s it. Other files need to be explicitly granted permission – which is (partly) what RW is doing with this error window.
But all the resources inside of the project automatically get permission. So, that should at least help this problem from happening to new resources.
Of course there are other ways that resources can get unlinked too – probably even some when the resources are in the project – but I’ll leave those uncommon corner-cases to the Realmac support folks.