Hey Matt,
Yes, first port-o-call was to clear cache's..
I believe I have found a limitation! All has been working fine up until last week when I added 2x more layers, taking this Map Config to 155 vector layers. This morning I totally re-built a new Map Config adding all 155 layers including queries, still they didn't appear in Left Panel. I then proceeded to remove 5x random vector layers from the same Map Config, and boom, all Queries on left panel are back!
Has anyone in the room got a Map Config with that many layers to verify?
Please note, each Department here in Council usually has up to approx. 100 layers in their go-to Map Config for their daily use, it is only about 10 users that choose to want to see the "All Data" (all layers) Map Config...