We have seen this behaviour with a couple of our testers during the Dorico for iPad 2.3 test cycle, but couldn’t (yet) figure out what the factors are in this behaviour occurring.
The good news is that the message telling you that the project has been deleted is incorrect, and it obviously shouldn’t be appearing. However, we’re not sure what is causing this incorrect message to appear: on some iPads there is an additional file notification being triggered, but as yet we cannot reproduce this at will.
We are all seeing the issue where files opened from iCloud Drive don’t appear in the Open Recent page of the Hub, and we will work to fix that as quickly as we can.
We’re sorry for the problems with file management in this version of the app. We will work diligently to resolve them as quickly as we can, but it’s a holiday weekend here in the UK so none of my colleagues are available to look into this until next week. I’ll provide an update as soon as I can.