Okay so I've been doing a bit of thinking and I've finally come up with the courage to write this 'theory' about why Twister is almost always missing at random times and when the Shadowbolts attack... And I think I found the reason why that is...

Maybe because... Twister is...

A Shadowbolt clone.

Think about it, In one of the previous chapters Luna said that she could see aura's and that Twister didn't have one. Maybe he doesn't have one because he is a clone that a Shadowbolt made to infiltrate the Wonderbolt's compound.

And that is why he sometimes goes missing, he needs to 'recharge' or something like that because the constant magic is too much work. The pony who created Twister might be a crazy pony too like Ruin or somepony else that hasn't been introduced yet.

I know that there isn't much to go on, but it is just an idea.
Any thoughts on this?

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Interesting theory. The Wondercast actually had a discussion about Twister earlier this month. Thought you'd be interested in listening in.