Please check if in fact the Documents/Publii catalog is empty – maybe it is just a lack of permissions to access documents (Publii should ask for it at start on macOS Catalina and if your refused the access – the app cannot access it): https://nektony.com/duplicate-finder-free/folders-permission
If the Catalina upgrade removed this folder content then the only solution is to start over again. Or check if you have any time machine backup made before the os upgrade.
For such situations we have created the backups feature – uploading input files to the server is not a solution as it will make sync process much longer and can expose non-public data.
Regarding WordFence – sorry – I have no idea what can be a reason, maybe your behaviours generates false positive alerts in this plugin.
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