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I believe you're correct - tokens won't work in the calendar file subject line. So you'll have to edit that file separately for each time you clone your program. As Frankly I'm amazed the tokens work in the body of the calendar file, generally speaking, tokens within tokens aren't really something that's supported in Marketo.
One caveat to using tokens in the body of your calendar token, if you haven't discovered this already: Any rich text tokens referenced within the calendar file will render the HTML explicitly on the calendar file. So any tags <h1> <p> etc will all show up in the finished product. Because of this, I find that I hand enter the content of my calendar tokens, rather than referencing other tokens within it.
Hope tis helps,