I have a mac with Asahi Linux (Fedora + KDE Plasma) installed, and I want to sync an Obsidian Vault through Syncthing. I use the mac GUI for Syncthing and Syncthingy for Linux. For some reason, it shows Disconnected (Unused) on both devices and the folders won’t sync.
If you mean that you want to use Syncthing to sync your files between the two operating system installations, then it’s not going to work, as Syncthing needs to have both of them running at the same time in order to perform the synchronisation.
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If you used a different, always-on Syncthing installation with the same shared Folders, that could work. You could do that “untrusted” so that the files were encrypted on that different installation.