Is this workflow possible?

I have SickBeard setup and I use iFlicks to take downloaded mkv file and remux them to m4v and add to iTunes.

However for certain shows, I also want to make a copy of the resulting m4v file and place it in another folder.

So, because iTunes is set to Copy file to the iTunes Media folder, the resulting m4v file gets called "<ep number> <episode name>.m4v", inside a "Season <x>" folder, inside a "<TV show name>" folder. It is the "Season <x>" folder that Hazel is watching.

It works fine, in that the resulting m4v file gets copied just fine to my chosen folder, but what I want to do is rename this copied file to <TV Show name>.S<season number>E<episode number>.m4v.

Example - a show called "Example", season 1, episode 1, episode name "My Episode":

1) SickBeard downloads it, filename Example.S01E01.mkv.
2) iFlicks watches the download folder and grabs mkv file
3) iFlicks fetches metadata, remuxes it, adds it to iTunes, deletes original mkv file
4) iTunes imports resulting m4v and renames it "01 My Episode.m4v"
5) Hazel copies "01 My Episode.m4v" to my chosen folder

The above 5 steps are what happens now, working fine.

What I want to happen is a step 6:

6) Hazel renames it to "Example.S01E01.m4v"

Unless the season and episode data is in the metadata, that data is lost by the time Hazel gets to it. It might be better to have Hazel copy the file before all that happens.

I think that info is in the metadata, but I'm open to doing it other ways

If it's in the metadata, then you should be able to use the rename action, putting the appropriate attributes in the pattern. Otherwise, you may need to get Hazel into the workflow earlier before the file gets renamed.