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I would recommend to try putting your char to sleep 3 days and then look for her at Dragons Reach, at Blades Hideout and at your houses. Worked for me.
In my case I started that companions quest and I had Lydia replaced too. After the quest I looked for her at my house at Riften and Whiterun without success. I tried Dragons Reach also and nothing. Then I went to the blades hideout (cos I recomended her to them) and she wasn't there too. Then I...