If the speaker doesn't know where another person is, but they wish they did know, would the following sentence be a good way to express this wish?
I wish I knew where you are now.
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In your scenario, the speaker doesn't currently know where the other person is, but they are engaged in the process of wishing that they knew where the other person is.
"I wish I knew where you are"
"Knew" is not actually indicating the past here, as indicated by "I wish" and "are." It is correct if used in the way that you described. This is a non-obvious and good question.
Note: BillJ pointed out that "I wish I knew where you were" is more natural, and I think this is correct for someone's current location. However, I think that "I wish I knew where you were" requires context to not be interpreted as someone's past location.
See examples here: https://www.google.com/search?tbm=bks&q=%22I+wish+I+knew+where+you+are%22