Ah right. I hadn't realised you meant controlled crying, I had assumed a gentle method because of her age.
In that case, did you set up an alternate mechanism for her to gain comfort and security in the night? I am thinking a snuggle toy she is really attached to, or a dummy, or both. Just something she can cuddle into when she needs some reassurance in the night if she wakes.
It sounds like you are her primary source of reassurance in the night. While all is well then she probably wasn't waking at all so didn't need any reassurance. But at the times when things are disturbed, she wakes and needs comfort, security and reassurance so she shouts for you.
I would set up a much gentler way to teach her that she doesn't need your reassurance to get back to sleep. Not by simply removing that comfort, but instead by slowly showing her that she needs you less and less.
A process called gradual withdrawal basically means giving her all of the reassurance she needs to be able to go to sleep in the cot, without being picked up, and stay giving that reassurance until asleep.
Then over time, slowly and gradually reduce the amount of reassurance she needs to get to sleep.
Reduce patting and shushing to just patting. Then just a firm hand on chest/back. Then firm hand at first, removed when settled. Then hand on chest briefly to resettle and retreat away from the bed, returning only if she stirs.
This is no quick fix. It will take time and patience. But rather than just removing her source of reassurance (ie you) this way teachers her she doesn't need your presence to feel secure and comforted, without denying her reassurance.
The good thing is that once done and out the other side, "revisits" after hiccups like your recent one are quick and easy to solve.