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Hi there. I'm Dr. Tim. Have you had her checked for a urinary tract infection? These can often start up after a stressful situation as she went through.
If she doesn't have an infection, there is a product called CatAttract which can help draw cats back to using a letter box. Also Feliway can help if the problem is due to anxiety issues.
And yes, if there is any way you can help her stay inside, if definitely try as much as you can. Nature's Miracle is great for getting rid of cat pee odor.....the smell often draws them back to pee again.