Edit Master Pages and other files on root

I have a simple question about templating nopCommerce. If I edit the Master Pages or the files on the root directory, will I lose those changes on upgrades to upcoming releases of the cart. If so how can I change the structure of the site without losing it to upgrades?

Thank you for you help.

really you can't

what you need to do is document the changes you make and remake them when you upgrade


keeping a track of the changes can save A LOT of time

Alright sounds good, I'll do that. Last thing I want to do is figure out what I did and have to figure it out all over again. Thanks for the tip.