I was thinking about how I might try and break out of a timeloop like that one, and the first idea was to try and force it to not be a loop, no matter how petty it was. My idea was, increment the loops. Just make a note of whatever giant number is spray-painted on the side of the Zephyr in the future, and then spraypaint the next-highest number in its place when you get back to the past. And then, just because the subtle difference that people are bound to treat loop twenty different from loop two just because they know how many there have been probably isn't enough, plug the incremented number into the computer as a random seed, so any calculations and simulations that use random values will come out different, and hopefully those will propagate and give some nice variation in the futures the SHIELD team encounters with every loop.
Other ideas: Daisy saw herself in a security video just from before the world ended. Cut or dye her hair, or get a prominent tattoo. It shouldn't take much to break history. Worse comes to worse, just go full Homer Simpson in the time of the dinosaurs and beat the crap out of everything you saw was intact in the future.
The problem with that is that it requires conscious thought and effort which runs you smack into the bootstrap paradox. A closed temporal loop as no "first time", just a four dimensional event horizon.
I was thinking of variations more at the quantum level. The exact locations of entangled particles across the entire universe, the exact path and spin of a single photon, that sort of thing. That may sound insignificant, but anything that's finite that can compound an infinite number of times can lead to exponential change and alter the probability curve.