I trade all the time as well. If you pause or stop the EAs, it will be harder to follow precise results after that. What if you are unable to do that one weekend? It will become a mess.
As Petko said the generator wors over all the Historical data. Now if you want your trades to close on Friday, you can select that when you generate strategies:
If you select it. You will generate strategies that actually closed on Friday. And you will have a better backtest.