I installed Google Drive Stream and used WinDirStat to compare what Insync had downloaded and what was actually in my drive. A number of folders, with no obvious pattern, were missing significant numbers of files or even folders.
None of them have multiple parent folders.
What I am going to do is delete the entire local copy and set up again and leave it running until initial sync is complete. Last time I did shut down the PC part way though.
Are there any limits to file size or number of files? For example caused by using 32 bit integers etc?