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RapidWeaver project files are actually a special kind of Mac folder called a package. You can actually right-click the project files and select to view the package content.

It’s the Mac OS GUI that makes these special folders(directories) look like a single file. External file systems (even the terminal on your Mac) process each individual file (could be hundreds) within the package (folder) independently, so the project file gets “out of sync” and becomes unusable.

Many other people have had issues with project files becoming corrupted and unusable when they store them on cloud services (Dropbox, OneDrive, etc) and NAS drives.

I’d suggest you keep RW project files on a local hard drive while working on it. As for backup, you can set up your NAS Drive to use TimeMachine. That gives you the an hourly backup(snapshot) for the preceding 24 hours.