How do I update customers cart prices and add discount and then let them checkout? I'm using Drupal 7 Commerce and Commerce discount, amongst many others.

So the use case is this. We often get enquiries for bulk orders containing many products. We want our customer to go to the website and add what they want into their cart. As admin I want to open that unpaid cart, edit product prices and apply a Fixed Price Discount. Then when the customer refreshes their cart they will see our amendments and continue with payment. Is this possible? Am I missing something obvious?

At present I can edit a order that is in the cart but when the customer refreshes their cart the order is reverted back to prior my changes. I can't edit product prices at all whilst the order isn't completed. Once in Completed status, I can tweak product prices and add the discount.

To get the Fixed price discount feature to work I had to switch from the Line Item Manager widget over to Multiple Inline Entity References. For the line items field on orders that is. Before that I couldn't use the Fixed price discount feature at all.

Any help would be greatly appreciated. I must be performing the wrong searches or something.
There aren't many good solutions here, because you're hitting up against the limitations of the pricing system. You have two basic options: custom line item fields that contain special pricing paired with a pricing rule that overrides the default product price or some combination of discounts that adjust product prices solely for that user. The former may be a challenge, because I can't remember if we ever fully got Inline Entity Form to manage line items, and the latter would be a pain for orders with a lot of different products.

The Commerce Price List module was ultimately developed to handle situations like this, where price lists can be assigned on a per user / quantity basis. It appears the same feature set works in D7 as in D8, but it would give the customer access to that pricing on any order while the price list was active, not just a single one. If that's no problem, then that's probably your solution.