I know you said it’s not an iCloud folder but to make sure since it hasn’t been mentioned––the macOS feature to “Optimize Mac Storage” (or other vendor smart storage type offering) has caused harm to Scrivener projects, including empty pages.
Excerpt by @kewms, Scrivener support:
Recently, I’ve seen an unusual number of support tickets that seem to be related to misguided “smart sync” operations. A “smart” sync is one that downloads files to the local system only when needed. Depending on your usage and the speed of your internet connection, though, this can result in the content of a file not being available when Scrivener needs it. Most people find the resulting “blank” documents extremely disturbing.
I also especially recommend against iCloud’s “Optimize Mac Storage” feature. There have been a few cases where this feature “optimized” projects off to the cloud while Scrivener was actively using them, leading to save errors.
From this recent post:
https://forum.literatureandlatte.com/t/switching-away-from-dropbox-what-should-i-know/123828/2