[Owen Smithyman]

This is an old thread, but I just ran across this very problem and found a wonky but free solution called multiAVCHD. https://multiavchd.deanbg.com/

It’s designed to allow footage to be played in Blu-ray players or something, but you can also use it to recreate the missing folder structure for your MTS files. Ignore the pages and pages of options. All you have to do is add your MTS files, choose an output folder, click the big Start button, and then click the small 1080p60 button (in my case at least). After a process during which Windows will probably mistakenly tell you that the program has crashed multiple times, your footage will be moved or copied to the output folder, which should have the correct directory structure.

Hope this helps!