First, in order to troubleshoot any possible bugs, please let us know what versions/commits of both MediaWiki core and Flow you're using.
If I understand correctly, it sounds like we might be talking about a few different things:
1. When you first go to a new board (you're about to create it for the first time) in a Flow-enabled namespace, it's normal for the board not to exist, and the tab to be red. See for example https://ca.wikipedia.org/wiki/Viquip%C3%A8dia_Discussi%C3%B3:This_doesn't_exist_yet?useskin=monobook (using Monobook skin to illustrate the tab is red).
2. If you previously deleted any content there, it will also be listed in the subline as you said. I have not heard of any previous bug reports where it would wrongly claim there was deleted content when it's a totally fresh location.
3. You said, "It appears topics also don't exist: Topic:Sn2g1yop0frbj7y7". There were bugs about this (topics being red), but they should be fixed in latest Flow.