We ended up doing a convoluted mess combination of notes in the notes field, refunds, and plugging in manual orders using our Square app.
We're also in the process of moving to BigCommerce after the holidays. This, among many issues, has been a complete and total dealbreaker for us. I had high hopes for Shopify, but they've ignored basic stuff like this for far too long, nickel and dime you to death for very basic needs that have to be farmed out to 3rd party apps, and in general seem to have zero interest whatsoever in supporting small to mid level businesses who do any sort of wholesale business. Frankly, we'd have been better off just staying on freaking etsy for the time being instead of wasting untold hours trying to make Shopify work properly.
Improved order management is a priority for us right now. Many of the new features that have recently gone in have been focused on order management (editing shipping address, editing order email, order tags, resending notifications, editable cart attributes) and the next set of features will be, too. Line item returns are currently in private beta. Better line item fulfillments, exchanges, and additions are to follow.
I have 3 web sites running on Shopify and I agree. I came from BC with all three sites. you get way too much functionality in BC then in Shopify. "Gift Certificates" FREE, Discount Coupons FREE. Calculated shipping FREE Option. however you have to pay for it here.
You really cant even print an order in shopify without and APP to design and invoice/print it.
Jonathan - Can you give us a date range as to when the new order management features will be available? 1 month, 2 months, 3 months, 1 year? This may help us determine if we continue with Shopify or not. At this point, transparency in feature releases and dates is probably key to keeping many of us around.