I've run out of junk for certain items and it didn't pull from any of the "more important" items. When you start building things, you'll see which materials are used to make your items.

In researching the related question How can I break items down into their components, I saw a complaint on Reddit to the effect that the extra, leftover materials get destroyed.

Why this is a common belief

Many people seem to believe this, and there's a good reason for that: it's confusing. And it's confusing for two reasons:

1. The composite item is removed from your character's inventory, but the leftover components are placed in the Workshop's inventory.
2. There's sometimes a delay before the leftover components reappear. If you want to speed up the process: go into Workshop mode, try to build something, and then exit. This appears to force the Workshop to update its inventory contents list.

Go, science!

I settled the question with science. I've tested this with various items a dozen or so times using the Armor Workbench, the Weapons Workbench, and the Workshop crafting menu.

The leftover components have always (so far) appeared in the Workshop inventory, but there's sometimes a delay.

Here's one of the experiments:

Experiment

• Remove all Lead from your inventory and the Workshop's inventory.
• Add two pencils to your inventory; each pencil has 1 Lead and 1 Wood.
• Go into the Wood Structure crafting menu—not to craft anything but just to check your Wood component count.
• Craft a Radiation Emitter, which among other things requires 2 Lead.

By creating the Emitter, we force the Workbench to dismantle the pencils, which liberates 2 Wood and 2 Lead.

If our Wood component count goes down, wood has been lost/destroyed. If it stays the same, our 2 "potential" units of Wood have simply been converted into 2 actual units of Wood.

Result

Our Wood component count remains unchanged. So unneeded materials are retained, just as though you'd broken the item down yourself.