I associated my account with another yahoo account, and after that I lost 50 reputation. Why is it so?
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Your reputation here doesn't get affected by association of your external accounts. It does get affected by your linking of your Stack Exchange network accounts. For example, I see you have >200 rep on Stack Overflow, and <100 rep here on Meta Stack Overflow. Try this:
You should be able to do the same thing on the Programmers SE beta. Please try that, and update your question if you don't get the expected behavior.