Why disputing incorrect charge on credit card lowers FICO score?

[Anonymous]

I posted this question in "rebuilding credit" but then realize it should probably be posted here instead. Your help/suggestion is appreciated. 

I have an incorrect charge by a unheard-of internet merchant on my BoA credit card (about $80). I filed a dispute and the merchant cannot provide verification and hence the charge is credited back to my account. BoA issued a new credit card but said my account is not changed in anyway.

Big surprise for me! My FICO watch score is lowered about 20 pts with a reason "Lost or Stolen Card" and "Consumer disputes this account information" besides the alert. Is there anything I could do to revert this report? As I understand this is not due to any of my fault... Shouldn't I be protected by identify theft? 

[AndySoCal]

When trade line is in dispute that trade line is not factored into the FICO score.  When the dispute is resolved the account will be included in the FICO score calculation.  Are you seeing two trade lines being reported one with the new account number and another with the old account number on the credit report?

[Anonymous]

Yes, I see 2 alerts (this I guess is what you mean by trade line). The first alert appeared when I started the dispute, and has dropped my FICO by 1 point. The second one appear recently after I received my new card, and has dropped my FICO by about 20 points.

Does this look normal? Why should I be penalized for identity theft, even after it has been validated that the charge was incorrect? I was told by BoA that even though I will get a new credit card, my account is not closed/changed and it shouldn't impact my credit score. At this point, what would be my best action to revert the alert?

[AndySoCal]

The fraud alert is not hurting your score. Do you see on the credit report one trade line (Bank of America) with the account reported as lost or stolen and another trade line (bBank of America) with the account number of the replacement account ?  The replacement Bank of America account for the lost or stolen credit card has the date open changed from the previous account?