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It would be in the best interest of your timing belt and the belt's pulleys to reinstall that upper timing belt cover. The covers are there for the purpose of isolating the timing belt components from the fog of very abrasive road grit that flies around the engine compartment while the car is in motion. With the cover(s) off, you are shortening the lifespan of you timign belt.LI_SHO:
supposedly it rots the belt. i left off the top timing belt cover after doing all the work...and i periodically check the belt for wear or anything unusual. nothing thus far!