You can remove a product through the order edit API by sending quantity: 0 for that line item. Unfortunately, at this time this will trigger a refund. I will bring this up as feedback for the team though.
Would love to see this improved! Also the docs are super confusing right now, at least in the short term those maybe should be updated. They list on edit order api docs a features to ‘Remove Line Item’ however there is no info on that, only info on removing the line item discount. Maybe removing the remove line item reference or at least specifying the method is just setting qty to zero would reduce confusion. Thanks!
Long term though would love better remove line item handling, we want to do an exchange in our case which is not easily doable with the auto refund. Thanks!