I had the same problem but I use both Mac and iPhone, and deleted the Logseq original folder twice, for the third run it didn’t create the “Logseq” folder, and my graphs didn’t want to synch with iCloud.
But I fixed the issue, by simply signing out of my iCloud from my iPhone. And the resign again. That refreshes or resets the iCloud synch. And after opening Logseq again it worked.