Last time I did evening EMH's was in July 08 at DHS. They restarted the fastpasses at the start of EMH's. They weren't an extension of the earlier passes. The original passes ended, and then new ones were started.
I remember this because Toy Story Mania had an insane line at the fastpass machine 45 minutes before EMH's started. The machines were closed, as they had run out for the regular park hours much earlier in the day. When we asked what the line was for, we were told that fastpasses would begin again for EMH's only, and people were in line for them. Craziness!
Things may have changed, as it was a while ago.