There are several reasons a thread may not appear in your Shortwave inbox. Here’s how to troubleshoot and fix these cases:
There are times where Shortwave needs to sync large amounts of data with Gmail, causing the Shortwave inbox to be slow to update. This can happen during initial import immediately after signing up, historic import after upgrading, or during a large bulk action. This is just a temporary disruption as the sync completes. It can take days to finish syncing in the very worst of cases, but your Shortwave inbox will eventually catch back up to Gmail and sync in near real-time.
Try revoking access to the other unused email services connected to your account. You can remove connected apps from your Google Account settings via Third-party apps & services > Access to > Gmail and by clicking "Delete all connections you have with [app]."
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