Developers and Valve are having some technical difficulties providing an upgrade option for those who owns the base game but want to upgrade to Digital Collector's Edition (it has Digital Comic Book which is exclusive to Steam version).
Steam Store also won't currently allow you purchase the Digital Collector's Edition if you already own the base game.
The (temporary?) solution:
The developer currently accepts user requests via e-mail. It should work like this:
- You send a message to firstname.lastname@example.org
with your proof of the purchase (could be order ID or Steam key, probably).
- The developer issues an invoice via PayPal and send it as a reply.
- After you pay the PayPal invoice, they send you a key for your Digital Collector's Edition upgrade.
The price for the upgrade may vary for different customers (first pre-orders vs indie bundles etc.) or it may be constant for everyone - this is something I don't know.
This may be obsolete in future, if they manage to fix the problem.