House Builder and House Builder Extension both make beeps. I found that House Builder Extension by D. Bur uses the same "House Builder" code. So when you install house builder extension, a copy of house builder .rb's get put in the "HouseBuilder" folder. I found the ui.beep code in the HouseBuilder folder, in the HouseBuilderTool.rb file, I changed ui.beep to #ui.beep in this file, and moved it down to the main plugin folder (over writing the other housebuildertool.rb file that got installed with housebuilder.

If you just modify the file in the plug in folder, housebuilder extension will still beep because by default it uses the one in the housebuilder folder.