The plugin mentioned (from Jeffrey Friedl) is 'donationware' so you can make a payment of any amount to him via PayPal. The resulting PayPal transaction ID is your plugin registration code, good until your Lightroom serial number changes.
Lightroom is not a browser like Bridge is or Windows Exlorer or Apple Finder. It does not show you all contents of a folder automaticaly.
The structure you want can be accomplished without draging or reorganizing. Just set up the importpreset (under destination).
Today Puget systems has made available a free benchmark for testing Lightroom Classic performance on Windows computers:
You don't know if it's related or not!
If i rename photo.NEF to photo.RAF outside Lightroom perhaps this is exactly what happens. That is what i meant, it is not possible to 'rename' an extension, inside or outside Lightroom. Yes technicaly you can do it but the file can not be used anymore...
If you open Lightroom and select the import option again. Do not click to start the import again, just look at the settings. Most likely that is what you used the last time. Maybe post a screenshot here.