Did you ever figure out what was going on?
I use the UnityAssemblies folder to build external plugins for my project. It looks like the folder is synced right before the script editor (Visual Studio) is launched. E.g. Assets->Open C# Project or double clicking on a script.
The Editor has an internal class (SyncVS) that syncs the VS solution, but you can't call it using normal methods. Maybe through reflection.
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