I was able to get sync setup reliability on my iPhone, iPad and MBP without trouble but I had to follow exactly the instructions below. I suspect you are but I thought I’d pass this along anyway just in case it is helpful.
To setup a synced vault through iCloud Drive:
- Start the app and choose “Create a new vault”;
- Name it the same as your desktop vault to make inter-vault URIs work;
- Wait for iCloud to sync this empty folder to your desktop;
- Copy and paste everything under your vault to this empty folder, this will now be your synced folder location;
- On desktop, using the “Open another vault” option, point to the new vault location in iCloud;
- Wait for iCloud to sync everything to your mobile device.