I'm guessing here that you don't type or read Hebrew, or really do much in the way of handling RTL languages. The rules that govern which-way-the-parentheses-point differ from place to place, here. Notably, the GREP query window doesn't use the same layout rules as your InDesign document. If my guess is correct, I'd suggest to you to simply rekey the GREP query, and copy/paste individual Hebrew characters from the PDF into the GREP query, without stopping in Word or in your ID layout.
(Or perhaps Save As Plain Text from Acrobat?)