@Prometheus labs CEO  
You’re actually correct in that the one “fixed” item is the tree of harmony, thus by extension, the ones involved in the timeline change and whatever tools are involved are retained and not removed.

@Daneasaur  
It seems the nature of time in the mlp world is paradox-proof in nature. My guess is how it does this is in the event that something happens that changes the timeline, even in a paradoxical way, instead of collapsing it partially disconnects whatever is responsible from the flow of causality, by making it so they can effect the timeline, but the timeline can’t effect them, so that way no paradoxes resulting from altering your can happen. Ex: you couldn’t cause a paradox by going back in time and killing you grandfather as you would be disconnected from the effects of the alteration you just made, basically making you an effect with no cause.

Hopefully Future Thorax does not meet his past self in this point in time.

@Daneasaur  
Reminds me of Doctor Who’s time travel rules, only less restrictive in that regard (You’re allowed to reshape the world without it breaking the timeline as long as its not a fixed point).

@Background Pony #A9A0  
You’re not wrong. MLP covers the implications of time travel very firmly in that you are either:
 
A: Making a stable time loop and changing nothing.
 
B: Causing a butterfly affect that reshapes the world.
 
There is no middle ground.
 
And doing the above situation would break everything. Seeing Discord as a friend would make Fluttershy less likely to put her hoof down in regards to Discord’s early betrayal antics. Seeing Starlight being a friend would make them more likely to trust her outright when they encounter her, resulting in a much more comprehensive loss for the Mane 6 when they encounter past Starlight.

As much as I love the concept of time travel, and I haven’t gotten tired of seeing it in fiction yet, I think whenever ponies mess around with time in MLP, it always ends badly.

Fighting his kin once again must be severely uncomfortable for Thorax. Who knows, he might even have to fight himself this time.