Reproduced with this as my entire modlist:
BASE: 3.7.1
Contenttweaker: 4.5.0
Crafttweaker: 4.1.6
JEI: 4.9.1.168

When developing my pack, I casually wanted to add a "rod" part to my mithril material. All seemed well, until I reloaded the game, and discovered that the mithril rod had not registered as an item. Weirdly, the mithril "crushed_ore", "crystal", and "dirty_dust" all registered just fine. All four of these items are added by the same line of my script, line 46. No errors were present in the crafttweaker log, and my scrublike perusal of the debug.log turned up no red flags.

Deleting the material_parts_contenttweaker.json and allowing the mod to generate a fresh one at startup seemed to resolve the issue, but I thought I would post relevant stuff here in case this is solvable/ a sign of something weird going on:

I created a clean modpack instance, with only the 4 mods listed above, and put a copy of my material system script, and copied over the material_parts_contenttweaker.json from my modpack, and launched it, and, again, the mithril rod, (on line 46 of the script, with all the other mithril parts) failed to register, even though the other mithril parts do.

My script: https://gist.github.com/TeetoKaziim/17c2ae707716e2d6ad05ca2a51f60907

My material_parts_contenttweaker.json from inside of config\acronym\saved : https://gist.github.com/TeetoKaziim/0940287eb9f093c52b184ba1a1604127

My crafttweaker.log : https://gist.github.com/TeetoKaziim/7d507004f34b98530073424586bc5b77

My debug.log : https://gist.github.com/TeetoKaziim/33689aadf98b221ac15656ce596f3df5 (592 kb i'm sorry mobile users.)

It seems like it's "something about that .json file" that keeps contenttweaker from updating it with the new part mapping, but I'm not cool enough to know what. Thankyou all for your time and consideration, and the best to ya.