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Make sure you clean the joint very well (with a stiff bristle brush) making sure you remove all dust and debris from the crack. Mix up some mortar and put it in something similar to a pastry bag (the thing bakers use to decorate with). A large Zip-Lock bag with a nipped corner should work. Squeeze the bag so the mortar fills the gap making sure the mortar ...
Use a Plugging Chisel. A plugging chisel has a tapered edge for cleaning out hardened mortar. The chisel is held with one hand and struck with a hammer. The direction of the taper in the blade determines if the chisel cuts deep or runs shallow along the joint.
You will certainly need to provide for some drainage of the now "lower" track of the window so that accumulated water can flow out. One thing to also consider is the overall design of the window itself. Many window units are designed with a definite UP and DOWN side to them. When you rotate such window by 90 degrees certain aspects of the window may be ...
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