Hello.
I have a similar problem. I just came back to office after working from home about two months, install new updates for macOS and also for all Affinity apps. Then my Publisher can not acces my documents in iCloud. I tried to figure out why, search the whole internet, whole affinity forum, find some treads, bot nothing was working for me. I am hopeless and angry because insted of working on a new large-size banners we need to print today I spend a half of my day by figuring out what is happening.
On my iMac the Publisher offers me to access Affinity Publisher Beta folder (I own publisher since the beginning) but in my iCloud Library this folder is missing and cannot be found by any Finder paths. On the other hand, on my MacBook, Publisher offers me to access Affinity Publisher folder (open context menu), where all of my documents are stored. In my MacBook the Publisher Beta folder is nowhere to be found and vice versa and my data does not sync even if I tagged it, it looks like that the directory for this folders are not in the iCloud anymore...
I tried to reinstall the app, sign off the iCloud, turn the Publisher iCloud Drive off.
Photo and Designer works great and I never experience such problem, but with Publisher I always can't acces the folder throught iCloud Drive, only from the app open window.
My devices:
iMac 27"—macOS Big Sur 11.2.3—Affinity Publisher 1.9.2
MacBook Pro 16"— macOS Big Sur 11.2.3—Affinity Publisher 1.9.2
Thanks for all responses.