can i control 2 Lutron swithes independently w/ Harmony 1000?

I think you have to step up to the more expensive Spacer system switches in order to have more than one switch work independently.

Otherwise you should be able to set up your scene (the memory for light level) to have one be all the way off and one be part way on, and then just send ou tthe scene command and both will go to their respective level. If you hit the all on, all off, bright or dim buttons it will end up controlling both dimmers though.

You might be able to run an IR emmitter seperately to each light and control them that way also. This would require an emmitter stuck tot he front of the switches though.