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CONTAINS SPOILERS:
I got this problem too and tried to find an answer on this forum some months ago with no joy. I think this is a rare problem, therefore.
This is how I solved it:
You have to get away from that map screen before the Harpers can intercept you. This took about 6-10 attempts but is worth the effort after all the hours you have put in to get this far. In the end I found it was best to run due north, immediately after speaking to the elf to get that major quest, and hope they don't catch you.
The problem is your reputation is too low. I collected all the quests I could in Chapter 2 but planned to come back later to complete them and pick up the EP once I had got Imoen back. Unfortunately, as well as increasing EP, many of those quests also increase your party's reputation so I ended the Drow chapter with a fairly average reputation score. This meant the Harpers didn't believe me and attacked; as you have also determined.
Once you successfully leave the screen without invoking the wrath of the elves get your reputation up as quickly as possible. A few quests and I got mine up to a much higher level. Then when you return and meet the Harpers again, they know of your good deeds and are prepared to hear your side of the story and, most importantly, do NOT turn hostile.
I have yet to complete BG2 BUT have been back to see the elves after being confronted by the Harpers and they are not red circled.
Hope this helps.
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