As per some recent comments on this thread, customers have confirmed that the issue is fixed.
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-InDesign TeamKitty Florido supported this idea ·Kitty Florido commented
1. Adobe InDesign 13.0/ macOS Sierra 10.12.6 (16G29)
2. No Application Frame, No Application Bar. Expanded Panels (above): Layers, Panels, CC Libraries. Expanded Panels (bellow): Align. Quit InDesign with the panels setup like the picture (or above) and restart InDesign.
3. Have the Layers + Pages + CC Libraries Panel expanded above Align.
4. Layers + Pages + CC Librares Panels hidden.
5. Attached a video and screenshots.
I believe InDesign closes the panel when updating the CC Libraries. I was able to reproduce it in a completely different machine, the common denominators are not having the application frame and have the CC Libraries Panel expanded. Hitting F7 to call the Layers Panel brings back the group of the three panels back.
The only plugin I have for InDesign is FontExplorer X Pro, and it's updated to the latest version. Also, tried it with and without the plugins. The result is the same.