The Time Loop resets all your progress and basically has you start over. But when you do a Time Loop, you earn Runestones based on your progress and you spend those on buying artifacts which grant you special powers and bonuses, making progress through the game a lot faster. I recommend going for the Time Loop at level 125 for the first time (as soon as you unlock the option), then go for it every time you hit a major wall and either upgrading your Heroes requires a lot of time and money, or the Boss really seems unbeatable. But the Golden Rule of Thumb here is to always Time Loop as late as possible in order to maximize gains.