After 4 hours of play with Janky Quality and multiple save/load cycles I've noticed some semi random recipes to make quality version of items/objects are missing. For example gun turret which I could swear I was looking at all quality versions right after researching them. Now only basic one is available. I took screens of all crafting tabs and I'll investigate over next hours of gameplay if anything changes with available recipes - if something goes missing for example.

https://cdn.discordapp.com/attachments/437305605686820897/1171890903770746930/image.png

Standard free play game (no editor), some basic mods included (rampant fixed, modular turrets, factorio-2ish modpack, alien biomes, bunch of QoL mods, bunch of UI mods). Before starting the playthrough and current moment I've disabled "simple landfill mining" mod and updated Janky Quality from 0.1.2 to 0.1.3

As mentioned, this mod wasn't tested with other mods, so compatibility issues are possible.

As for remediation, first try this Lua command:

/c game.player.force.reset_technology_effects()

Second, is that assembler a normal assembler or one with quality modules in it?

Its a normal assembler 1, gray one. I haven't even researched quality yet, nor used it. I tried the same thing in blue assembler 2 - seems its the same.

Funny thing is, science packs are not modified by any of the mods I'm using (when moused over - it doesn't give mod name in blue as if it was overwritten by any od the mods) - yet red one has quality version, green doesn't, blue and military have quality versions. That's why it seems random.

Similarly - long handed inserters or yellow belt undergrounds/splitters didn't get quality versions. Yet red belts and all of their version did get quality versions. Those are "overriten" by "ghost on water mod" though - so can't be sure of anything, BUT...
Normal ammo magazines have quality, piercing ammo didn't get quality. None of them are overwritten by any mods.

It almost looks like quality "disabled" itself during some of the researches, but worked fine with the rest. I disabled Janky Quality for few minutes when it refused to load game after upgrade from 0.1.2 to 0.1.3, but never loaded the save file or saved the game with JQ disabled, so its not a possibility.

Using the command actually did more bad than good. It removed more recipes instead of restoring missing ones. For example it removed military and chemical science quality versions (they were there before command) instead of adding quality to green science (it was missing quality versions for some time). Reloading the save and using the command makes exactly the same recipes disappear - so its not totally random.

/c game.player.force.reset_technology_effects()
is not the solution that works for me. It makes things worse.
https://cdn.discordapp.com/attachments/437305605686820897/1172062387734593536/image.png

I've also started brand new game with exactly the same set of mods (just way easier map settings to speed things up) - I'll try to pay attention to WHEN recipes start to disappear. As of now (1h gameplay) all of them are still there, including the ones that went missing in original playthrough.

Edit:
I've disabled all the mods to use the command and see if it restores vanilla item quality recipes - it DOES NOT.
With just normal vanilla game and all mods but JQ and the required lib disabled - the command does not return the missing quality recipes into the game. Moreover - it still REMOVES some of the recipes that were there before command (same effect, same recipes as with others mods on).
https://cdn.discordapp.com/attachments/437305605686820897/1172066589089202196/image.png

New development. Either the command is a bust of the mod has a serious problem.

1. Disabled all the mods but base (1.1.94), flib (0.13.) and janky-quality (0.1.3)
2. Started new "vanilla"-ish world with just those three mods.
3. Setup science to rush research Automation and green science.
4. Used the command to reset tech effects.

Result:
Recipes for quality versions of: Green science, long handed inserter and assembly machine 1 got removed.

https://cdn.discordapp.com/attachments/437305605686820897/1172081041498984458/image.png

I'm reporting this because it was mentioned in another thread that "It seems to be an intricacy between Editor Extensions and how I do tech. It works fine in the normal game."

Major fix was just pushed. It should fix your science unlock issues. Let me know if it works!