I have noticed that when the machines are removed they are gone from the inventory and I have to craft them again. So I checked the code and found they are actually returned to inventory as assembly machines :O

a small change fixed it :
entities.lua
(Line 8)
From :
minable = {mining_time = 1, result = "assembling-machine-2"},
To:
minable = {mining_time = 1, result = "auto-barrelling-machine-1"},

(Line 90)
From:
minable = {mining_time = 1, result = "assembling-machine-3"},
To
minable = {mining_time = 1, result = "auto-barrelling-machine-2"},

Thanks for the mod very helpful with the zillion liquid recipes in angel mod.

Yeah, it's not a bug.

Since I've decided to make them easier to make in just requiring an Assembly Machine 2 or 3, I didn't want to add two more recipes just to convert them back to the original Assembly Machines.

If you feel like it would be better to have them permanently changed to Auto Barrelling machines, tell me here and I'll think about it. It's definitely a clarity thing.