how do i undo "recreating enclosing folders"?

I accidentally ran "git clean -f" at the root directory of my terminal and lost a lot of files.

So, I restored my computer's hard disk from a previous time machine backup. It copied 400,000+ items overnight and in the morning I pressed the option to replace the old contents with the new. Then I pressed the "recreate enclosing folders" by habit and not actually reading what it said. Now I have lost all backup versions in Time Machine. Is there any way to reverse this restore?