Scrivner does not allow saving to a projects's.scriv folder

I have reverted back to scrivner 1 but am having trouble backing up my files. I get the following message: scrivner does not allow saving to a projects’s.scriv folder
I get this whenever and where ever I try to back up a project.
Can some one please explain what has gone wrong and how to put it right?

Use a separate folder for your backups, since you can’t save to the scriv folder. That folder is for the actual project and nothing else.

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In addition to the terrific advice from @Sanguinius, I recommend you make sure that the folder you pick for backups (I use ~/backups/scrivener on local disk) is indeed backed up by whatever you use to backup your computer.