I made some wooden crates, then upgraded to metal ones, which involved emptying the wooden crates. The wooden crates, which now show Empty, cannot be used to craft metal crates.

Is this specific to Sky Factory 4's custom recipes or the built in defaults? If you're using the built in ones, try using build 0.0.22 (tested and worked) otherwise it's up to the SF4 configs to fix.

I didn't realize SF customized the recipes for the Crates, I'll refer it to them, thanks.

@Funwayguy I'm curious as to why when a crate is first crafted it has NBT data:
<bdsandm:wood_crate>.withTag({crateCap: {maxCap: 1024, objColors: [-1, -1] as int[], oreDict: 0 as byte, overflow: 0 as byte, refStack: {id: "minecraft:air", Count: 1 as byte, Damage: 0 as short}, count: 0, locked: 0 as byte, stackCap: 64}})

If you place it and pick it back up the NBT stays the same, but if you insert and item and remove it then pick it up it has a different count:
<bdsandm:wood_crate>.withTag({crateCap: {maxCap: 1024, objColors: [-1, -1] as int[], oreDict: 0 as byte, overflow: 0 as byte, refStack: {id: "minecraft:air", Count: 0 as byte, tag: {}, Damage: 0 as short}, count: 0, locked: 0 as byte, stackCap: 64

The problem still exists (SF4). Not sure why it would be SF4 problem to reset the tags when the crate is emptied?