I couldn't put the dust covers back on after I installed them. I did some research on here and on other sites and it seemed they weren't really critical, unless driving in heavy dust environments. That said, I have taken the car through some incredibly dusty conditions without the dust covers and haven't had any issues. The LED's I used have a fan on the back and require airflow. I had intended on getting some rubber "universal" type covers so I could seal them back up but haven't gotten around to it--yet.
I bought the car with a single burned out low-beam and fog lamp. The high-beams were still good. I never use the high-beams anyways, but, I also needed to be cost effective because when I replaced my lamps with LED's I was also doing a brake upgrade which absorbed much of the funds available. I'll get around to getting the high-beams replaced when one burns out, though. Probably at that point I'll get new universal type rubber dust caps for them too.