Smart Gallery tagged iClone content as being "Not Installed" even though it was correctly installed. Despite this I double clicked on the Packs in the SG to get the content redownloaded in the hope that it would solve the issue.
That was my biggest mistake, and here is a short list of some of the things that have been messed up.
G5 MixMove_Male and G5 MixMove_Female motions are now stored in my Character folder
LoPoly_Medieval Characters are now all stored in the root of the Character folder, even though I already had a Sub-folder there from the original install containing them.
The props from the Medieval World Builder pack are now stored in the root of the Props folder, and not in the Sub-Folder that already exists.
The same happened with the Small Crowds Medieval Witch Hunt pack.
The HD Sky Props are saved correctly in my Props folder but the "Smart" Gallery has reinstalled them in the root of the Sky folder - and they don't show there inside the Content manager in iClone because of the missing iSky name
I haven't done a 100% check of all folders yet, but the above issues are so far the most obvious errors caused by the SG.
System: Win 10 Pro (1909), Asus X99-E WS, CPU i7-5930K -3,5 GHz, 32 GB DDR4 2666-16 RAM, NVidia GTX 1080 Ti GPU - 11 GB VRAM(Driver Studio-442.19), Samsung 850 Pro 512 GB SSD, 6 TB HD storage.