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Suppose so. But if you were happy in your job and happy with getting citizenship why not stick with it? I guess my thoughts are that if she was always planning on using GB citizenship to get a job in the EU, it's not completely a Brexit issue that she's gone - she would have gone anyway. To up and leave before having any idea what will happen after being excited to get citizenship seems to be over-reacting.
But anyway - I don't know her circumstances so it matters not.
Just my 2p but, if you became a UK citizen so you could work here and in the EU then it seems like a sensible move to start looking at establishing yourself in a country that will stay in the EU.
The timescales around our exit are likely to be a decade*, but you never know. So what have you got to lose by securing your position now. She can always come back.
*my guess