Ok, so this is strange - last week I purchased a S20 + and transfered my data using Smart Switch. Everything was working well until this morning when I noticed that the very same folders that duplicated apps on the S9 also had duplicate apps in them on the S20. I manually removed each duplicate app and then cleared the cashe partition, when I rebooted all those apps and the folders they were in had vanished (but not ininstalled). So I had to place them back on the home screen and then create the folders again.
So I've obviously transfered the problem somehow from my old S9.
Oh😅 i understood that you had the problem but you solved it 😅
Well you can hard reset your phone and manually transfer photos on your pc and use cloud to save app data.
Then you import everything manually. I never use smartswitch when i reset but install and set up everything from stratch