I would say spend as much time as possible with her downstairs until she trusts you completely. Brush her, love on her as much as possible. Also light massage is good especially around the ears. Hopefully she will want more and make her way upstairs. She probably needs to build trust. My kitty never did overcome the fear of thunderstorms and always hid under the bed so I made her a comfortable spot to lay in under the bed. If you do have to put her in the cat carrier try putting her in backwards then she won't know what you are doing until it is done. Good luck.
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