Is punctuation required between the repeated in's?
"...users who are still active yet haven't logged in in more than x days..."
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No, that sentence is OK, as is. It just looks odd. Punctuation would only make it look odder.
On the other hand, when I am writing and run into circumstances like that, I try my best to find another way around the double-word.
This is how I would handle this one:
"...users who are still active yet haven't logged in for more than x days..."