tl;dr
For the past several seeks I’ve been noticing that when Pull Requests are Closed at the GitHub layer, Issues that are linked to such a PR at the GitHub layer are no longer transitioning automatically to the Closed pipeline at the ZenHub layer. This transition used to used to happen reliably, so I’m curious if this is a bug or if there was an intentional change in functionality that I missed.
Details
An example of a public Issue where I recently observed this is panic: (*vng.Array) when running JSONBench q2 against CSUP in vector runtime · Issue #5734 · brimdata/super · GitHub with its linked PR vng.Metadata: Encode null for unsupported values by mattnibs · Pull Request #5736 · brimdata/super · GitHub. As I write this post, the Issue is still in the “New Issues” pipeline despite the both the PR and Issue having recently been Closed in GitHub. If anyone at ZenHub wants to sniff around in our config to investigate whether there’s a bug there, you certainly have my blessing. 
Here’s why this matters to me as a user. In the past I settled on a workflow in ZenHub for “verifying” the fixes of Issues. Using GitHub’s “Development” settings, our developers reliably link their PRs to the Issues they’re intended to fix, so when such PRs would Close in GitHub the linked Issues would automatically Close in GitHub and in turn this triggered the automatic transition to the Closed pipeline in ZenHub. Therefore I could find all the recently-closed issues at the top of the Closed column in ZenHub’s Work Tracker view. After verifying that the fixes of all those recently-closed Issues were solid, I’d write down the Issue number of the last one I verified, so the next time a bunch of Issues closed again, I’d know that any Issues in the Closed column “higher up” than the one I left off with last time are now ready to be verified.
Now that the transition is no longer happening reliably, I can’t rely on this workflow anymore. Instead I’ve ended up going into the GitHub Issues list for each repo and querying “is:issue sort:updated-desc state:closed” to see which have been recently closed at the GitHub layer. But the workflow at the ZenHub layer was vastly superior because it allowed me to see the recently-closed issues across the multiple repos in my Work Tracker view.
Hope that makes sense. Thanks!