Fusion saves all data/models online, means data/models are not on your computer, they are saved in cloud repository. That's why data are accessible also via web A 360 (myhub.autodesk.com).
Only when you work in offline mode a saved files while in offline then data/models are saved locally on your PC (data will get into cloud when you switch Fusion online - data get uploaded into cloud). So by cleaning recommended folders you will loose data created/saved in offline. But I suppose you work in online and all your data are in cloud, so you are not going to loose them.
For sure, you can export file as F3D to local drive (open file, from main menu File -> Export. Later you can import them File -> New Design From File or upload them.
Fresh installation: from Autodesk web page http://www.autodesk.com/products/fusion-360/overview
Complete instructions: https://knowledge.autodesk.com/support/fusion-360/troubleshooting/caas/sfdcarticles/sfdcarticles/How...
Regards
Jan Priban
Autodesk Fusion team