Great job with all the testing and figuring this out guys!!! My hats off to you!

Thank you everyone for all the replies. I had read that it gets lost and read that it stays.. I've been manually scrapping but it's slow going. If that's the only way to keep everything, however... It's unfortunate we have to do it manually, I just want a square = scrap all junk option. Bethesda, please! <3

YES! Only not square since I'm on the PC. How they could not have this is beyond me. I've spent a couple hours last night just dropping/scrapping/transferring all my craftable materials just to have everyone in one nice clean spot (Red Rocket shop). Now I just have to find more wonder glue and duck tape (yeah I know I can grow crops to make adhesive, but if I wanted a farming simulator I would have bought one).

This was a really helpful thread, thanks to everyone who did the testing!

FWIW - I'm sure the mod community will add some "scrap all" functionality soon enough.