GameVersion: 0.17.43
ModVersion: 6.1.2
Modlist: pastebin VzsqYbpW
Log: pastebin jpRzuCuG
Symptom: no first tier vanilla mini machines
fix attempted: yes

Diagnosis:
When the machines are unmodified it seems to set their name and icon back to being what they were copied from, and registering them as a duplicated recipe thus breaking the dependencies of later tier mini machines, this seems to only occur when no values of the copied tier 1 vanilla machine are modified from what they were copied from, save the name and icon. this seems to happen irregardless of the mods that would be modifying said machines being active or not in load order.

Okay, I'm not sure if I'm following you... something about duplicating recipes makes t1 mini machines not appear in the crafting menu? If something is modifying mini machines after it's already completed its scripting, then I probably just need to add an optional dependency.

You have so many mods that it's hard to actually pinpoint which one of them could be causing issues. I know AAI, Bobs, and Angels are all working together properly, from what I could tell. But I need to know how to recreate this issue in order to fix it. Settings in mini machines are also important, if changed from default.

looking at the logs the only things that run after the data-final-fixes script that could possibly touch it is space exploration. and the issue is the t1 mini machines get reset to be, for instance with assembling machines, another copy of "Assembling machine 1" with the list of parents being the only differentiation, however even with space exploration and several other that would change the base item of "Assembling machine 1" it still occurs, the only thing that i managed to do to restore it to "mini assembling machine" was change the "burner assembling machine" to "stone furnace" just as a test. (the only change i made to a test copy, returned to the official version of the mod when i posted this thread)
all settings enabled, save balance

Okay, I see the issue now. I always have the balance setting enabled, which doesn't appear to have this issue. So the t1's are copying the recipe, but then not changing anything about it. The t1's still exist in the game, but simply don't have a crafting recipe associated with them. And the t2 and up machines are all working properly. And doesn't happen in vanilla, only when modded.

Hm, that's definitely weird, I'll take a look and see what's wrong.

EDIT: Okay, this seems to be a problem with AAI specifically; bobs+angels still works fine in all other cases.

Alright, AAI compatibility should be fixed as of v6.1.3

Also figured out this issue has been in present for over 4 months, considering this post describes most of the same symptoms. Many thanks for actually helping me resolve that longstanding issue as well!