When you are done inside the clean boot and you are going to restart the computer again, then you can enable them all again.
Yes you have to enable them all again, otherwise they will never start.
But you can enable and disable all the files in the task scheduler in a faster way, by selecting them all at once and then choose disable / enable, like in my picture.
This is if you have windows Vista, 7, 8 & 8.1
Tomas