This happens in code and also using the latest SharePoint Search Query Tool (v2.8.8, https://github.com/pnp/PnP-Tools/releases/tag/v2.8.8-Search-QueryTool)
I do a query (Example "UniqueId:"{67286CE0-AA7C-4779-B220-9241FDB17C19}"" and it retrieves the file with that ID. I do another query for a different file with the correct UniqueID, and the ResultTable Row count is zero.
Is anyone else having a similar issue? It seems to be happening on several document libraries in my tenant. I can't find a patter as to the files it can't find. Some have been there for a while, some are new, and some a recently updated.
Searching by UI on the site seems to retrieve them, although at that point I'm not specifying UniqueID, just entering the guid in the search box.