Each profile has its own set of bookmarks, passwords, etc. Sync is also a per-profile thing.
I can look to see if there’s a Chromium bug about this. If this affects enough people, it should be fixed in Chromium and we’ll get the update and we can release a new version of Brave with that Chromium version.
Definitely, I would recommend making a ZIP file of your profile directory. Everything is still there. There must be a permissions issue though. Try some of the steps for the sub-folders. For example, look at permissions for %LOCALAPPDATA%\BraveSoftware\Brave-Browser\User Data\Default folder. Or for one of your profile folders (ex: %LOCALAPPDATA%\BraveSoftware\Brave-Browser\User Data\Profile 1). Your account should be the owner for these folder - and you can propagate the permission to all child object.