I found the issue: glass_bottle_chaos_essence.json uses the Forge blockstates format, but it's located in models/item so Minecraft tries to parse it as an item model rather than a blockstates file. It doesn't have the "parent" or "elements" properties, so it gets parsed as a model with zero elements (annoyingly, Minecraft doesn't detect this as invalid and throw an exception). Since there's zero elements, there's nothing for Minecraft to render and the item appears invisible.
You need to move glass_bottle_chaos_essence.json to the blockstates directory. As I said in my previous post, you also need to move standard_item.json to models/block (or a subdirectory) to it can be used by blockstates files. It should also extend minecraft:item/generated instead of copying it.
Another issue I noticed is that you're passing null as the CreativeTabs argument of Item#getSubTypes even though it's marked as non-null (by the @ParametersAreNonnullByDefault annotation applied to all vanilla packages). Your IDE should warn you about nullability issues like this. Use CreativeTabs.SEARCH as the default tab for Item#getSubTypes.
I also recommend annotating your event handler classes with @Mod.EventBusSubscriber rather than manually registering them with the Forge event bus, but this isn't required.