@Clara Cleverence 

"The issue is that QuickBooks isn't really built to handle inventory adjustments to COGS directly, which can be kind of a pain since it sees cogs as an operational expense, not an item-level cost adjustment."

QBD can handle inventory adjustments to COGS just fine.  It's not a pain at all.  Just select COGS as the adjustment account when making an inventory quantity/value adjustment.  This is, in fact, an item-level adjustment.  Have you used QB Desktop?  

"Here's what you wanna do: make sure your adjustment account's set up right for handling non-operational cost changes. I'd say setting up a special "scrap adjustment" account could be smart. Maybe stick it under "other expenses" or a special "inventory adjustments" category, so your operational costs stay neat and you get a clear idea on scrap losses."

Yikes!  Scrap is an operational expense and part of COGS.  Recording it as a non-operational expense (other expense) is very wrong.

BTW, why are you posting to a thread that's over 5 years old?  This creates unnecessary clutter in the forum, especially when the advice is misleading.