Before I start, I had these issues the last two times I tried to come back to Orion in the last one and a half years. Sync with iCloud unfortunately was always an issue.
What worked for me, after coming back to Orion again some days ago, was to really delete everything manually and start from scratch, forcing one coherent state across my Mac and my phone. I struggled a lot with the iCloud data being corrupted. I started with a clean Orion installation and tried to force this new and fresh state into my iCloud. However, when fetching this state on iOS, I could see tab groups I had created for very specific projects more than one year ago reappear. "Force fetch from iCloud" on iOS was indicating that it was loading like 10,000 bookmarks, although macOS told me just 5,000 were uploaded.
I don't know what it is, but Orion struggles to clean up the iCloud state for some reason. Hence it needs a little bit of help.
What really helped was deleting everything from iOS, in the hope it would really delete my data from one year ago that the browser on macOS was not displaying at all. Somehow the iOS app has access to data that Orion on Mac will not see, hence I force-synced the local state of iOS to iCloud. After that, I deactivated everything for iOS and deleted the app again.
Going back to macOS, I was backing up all the data and after that deleting everything—bookmarks, iCloud data, caches, everything (see https://help.kagi.com/orion/misc/technical.html). For this step, really make sure to have backups of your bookmarks and so on.
After this step, I had a clean installation of Orion on macOS. Out of despair, I turned syncing on and off so many times, just to be sure to resolve any issue with iCloud (I followed https://help.kagi.com/orion/support-and-community/troubleshooting/troubleshooting-syncing-data-issues.html).
Finally, I invoked "Force sync local changes to iCloud" (many times) until iCloud accepted this to be the real state. During this process, I could see the iCloud icon with an exclamation mark next to the reload page button in Orion on macOS appearing with an error like CKErrorDomain 6. After some waiting (maybe an hour) for iCloud to finally catch up and the error to disappear, I could also see that the space occupied by Orion in iCloud (Save to iCloud) got way smaller.
Now I reinstalled Orion on iOS and used "Force Fetch from iCloud" to see if anything shady appeared. Next, I imported my bookmarks to macOS, force-synced to iCloud, and fetched again on iOS. Now the numbers of bookmarks uploaded and downloaded aligned.
Now it seems to work without any force fetching—new tab groups and tabs appear in real time when I hand off from macOS to iOS. I am not sure how long I can keep this all stable.
I might be missing some details, and there might not be a very clear structure to it, but this is what helped me resolve this issue as old as two and a half years.
macOS: 15.6.1, Orion RC Version 0.99.138-rc (WebKit 623.1.8.0.0)
iOS: 26.1, Orion TestFlight 1.3.31