I had two tinkers' tools with soulbound and my armour had the soulbound enchantment from EnderIO. I was not wearing the armour, it was in my inventory. These items were removed from my inventory and didn't drop when I broke my gravestone.

The items were obviously saved in the death inventory save (as I used this to get them back), but not in the grave save.

Unfortunately, it's not something we can fix on our side - grave just stores everything it gets, but actual contents are depending on other mods' handlers that run before it. We have small manual on debugging graves here.

@TheRedMelon Where you using SpongeForge at all? We have had reoccurring issues regarding graves and correctly recording item drops with them, and are currently investigating issues with other grave mods.