Flash can take command-line arguments. So you can do os.system("flash.exe myFileToOpen.fla") . That'll open Flash and have it open the document "myFileToOpen.fla".
If the FLA is in a different directory however, you'll need to give the path in front of the filename in the command line argument. It can be relative or absolute. And if it contains spaces, you'll need to wrap it in quotes.
# absolute path and with quotes because of spaces
os.system("flash.exe 'C:\the\directory\to my file\here.fla'")
# or for relative, using just the .. syntax