All the Brachos Bilam gave eventually were reverted back to curse except for Ma Tovu, the bracha praising our shuls. Why was this the lone exception? The Yaaros Dvash explains that the reason the brachos did not have any long lasting effect was because Bilam meant them to be curses. This refers to any of the greatness he prophesized about Bnei Yisroel's kingdom and glory, which he really did not want to materialize.
However when it comes to the Bais HaMikdash all the bracha in the world comes to all the nations via the Bais HaMikdash. Chazal tell us that if the nations knew how much the Bais HaMikdash benefited them they would not have destroyed it. They would have placed armed guards around it to protect it.
The Bracha from Bilam of Ma Tovu was the lone Bracha that he said with any amount of sincerity since deep within it lay his own good and not just Klal Yisroel's. Therefore this bracha remained.
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