https://photos.app.goo.gl/eK1PyRjWwuvWo9dx8

I'd need more information, like, why do you consider that recipe to be broken?
but looking at the screenshots, you have multiple different mods installed there. I'd need a complete list of mods to figure out what's going on.

here is a mod list
Actual_Craft_Time_0.5.9.zip
adv_heat_1.3.2.zip
angelsbioprocessing_0.7.17.zip
angelsinfiniteores_0.9.8.zip
angelspetrochem_0.9.14.zip
angelspetrochem_0.9.15.zip
angelspetrochem_0.9.16.zip
angelspetrochem_0.9.17.zip
angelsrefining_0.11.19.zip
angelssmelting_0.6.14.zip
AsphaltPaving_1.3.1.zip
AtomicArtillery_0.2.3.zip
attach-notes_0.5.0.zip
auto-research_5.2.1.zip
AutoDeconstruct_0.1.21.zip
Automatic_Train_Painter_1.1.2.zip
BatteryLocomotive_1.2.0.zip
blueprint_flip_and_turn_101.8.6.zip
bobassembly_1.1.2.zip
bobelectronics_1.1.3.zip
bobenemies_1.1.1.zip
bobgreenhouse_1.1.0.zip
bobinserters_1.1.0.zip
boblibrary_1.1.2.zip
boblogistics_1.1.2.zip
bobmining_1.1.1.zip
bobmodules_1.1.2.zip
bobores_1.1.0.zip
bobplates_1.1.2.zip
bobpower_1.1.1.zip
bobrevamp_1.1.2.zip
bobtech_1.1.2.zip
bobvehicleequipment_1.1.2.zip
bobwarfare_1.1.2.zip
Bottleneck_0.11.7.zip
BuilderBotStart_0.3.1.zip
capacity-combinator_2.0.0.zip
capacity-combinator_2.0.1.zip
capacity-combinator_2.0.2.zip
ChunkyChunks_1.5.0.zip
CleanFloor_1.1.0.zip
combat-mechanics-overhaul_0.6.15.zip
copy-recipe-to-chest_0.0.1.zip
CopyAssemblerPipeDirection_0.1.4.zip
CreativeItems_1.6.0.zip
DeathMarkers_0.4.0.zip
Deep_Storage_Unit_0.1.10.zip
DefaultTrainConditions_1.1.0.zip
Electric_Transformators_2.1.1.zip
electric_water_boiler_0.0.19.zip
EnableResearchQueue_1.0.4.zip
EnhancedGridEnergyStores_1.110.1.zip
even-distribution_1.0.7.zip
Factorissimo2_2.5.1.zip
far-reach_1.1.0.zip
Fill4Me_0.10.0.zip
flib_0.7.0.zip
Flow Control_3.0.8.zip
fluidTrains_1.0.0.zip
FluidWagonColorMask_1.1.0.zip
FNEI_0.4.0.zip
FreeCable_1.0.2.zip
Full_Power_Coverage_1.1.0.zip
Full_Power_Coverage_017_0.6.0.zip
GCKI_1.1.1.zip
GDIW_1.1.0.zip
helmod_0.12.5.zip
Hiladdar_Scrubbers_1.1.0.zip
Honk_4.1.1.zip
IslandStart_1.1.0.zip
KS_Power_0.4.1.zip
LandfillPainting_0.5.0.zip
LandMover_0.2.8.zip
laserlines_0.3.1.zip
LoaderRedux_1.7.1.zip
longer-belts-redux_1.1.0.zip
mod-list.json
mod-settings.dat
Mud_WaterWell_1.6.0.zip
NepgearReNepped_1.1.5.zip
nixie-tubes_1.1.2.zip
Noxys_Trees_0.4.0.zip
Nuclear Fuel_1.1.5.zip
Nuclear_Operators_Utilities_1.2.0.zip
PickerAtheneum_1.2.4.zip
PickerExtended_4.1.3.zip
PlutoniumEnergy_1.2.4.zip
Portals_0.7.0.zip
power-combinator_5.0.0.zip
power-combinator_5.0.1.zip
power-combinator_5.0.2.zip
power-grid-comb_1.1.0.zip
pushbutton_1.1.0.zip
remote-switch_2.0.5.zip
reskins-angels_1.1.2.zip
reskins-library_1.1.2.zip
resourceMarker_0.7.25.zip
reverse-factory_8.0.2.zip
RITEG_1.3.3.zip
Robot256Lib_1.1.2.zip
rso-mod_6.2.2.zip
sane-concrete-017_1.1.8.zip
SchallCircuitGroup_1.1.0.zip
SchallRadioactiveWaste_1.1.0.zip
SchallTransportGroup_1.1.0.zip
simhelper_1.1.1.zip
Squeak Through_1.8.2.zip
stdlib_1.4.6.zip
steamTrains_1.1.0.zip
SteamTrains-Graphics_0.1.1.zip
StoneWaterWell_1.20.1.zip
textplates_0.6.3.zip
timeseries_0.3.4.zip
TLBE_1.4.0.zip
upgrade-planner-next_2.2.1.zip
UsefulCombinators_0.4.7.zip
VehicleGrid_1.4.0.zip
VehicleSnap_1.18.4.zip
VoidChestPlus_2.4.0.zip
walls-block-spitters_0.6.2.zip
Warehousing_0.4.1.zip
Waterfill_v17_1.1.0.zip
WaterWell_1.1.2.zip
YARM_0.8.203.zip

In short, when I disable this mod a critical crafting recipe gets renabled. under plutonium energy, the mod, a research called plutonium processing needs a crafting recipe called advanced nuclear reprocessing to get Plutonium-238 does this help?

That's a lot of mods.

Though, I think we can narrow it down to an issue between Plutonium Energy and Bob's MCI, However, It's also possible Angel's mods could be part of this issue too.

Looking back at your screenshots, the only mention of my mods is my library editing the technology.
The library doesn't actually change anything important, it is likely the redundant prerequisite cleanup script, removing a prerequisite that is already met, because it is a prerequisite of one of the other prerequisites.

Talking with the Angels team, they asked if you could turn off as many mods as possible, to find the minimum number of mods where the issue still happens.

I have had a look at this and for the life of me, I cannot get the mod mix/settings to match your screenshots. Can you please link a save file I can sync to?
I am also seeing that you are not running all of the mods listed above or are running some obscure seldom used settings. I am willing to diagnose the problem, but the information in its current form is less than helpful.

I can confirm that boblib is only removing uranium-processing as a pre-req (as it is a pre-req of the other pre-req)... What im not seeing anywhere, is why that recipe no longer has a recipe unlock.
If I disable the pre-req trimming function the recipe is still missing. Im digging a bit deeper.

FOUND IT!!!
PlutoniumEnergy in data-updates on line 7 removes all effects from that particular technology...

if mods['bobplates'] then
    -- Disable some recipes
    data.raw['technology']['plutonium-enrichment-process'].hidden = true
    data.raw['technology']['plutonium-atomic-bomb'].prerequisites = {'atomic-bomb'}
    data.raw['technology']['plutonium-processing'].effects = {}
end

I don't know why he did that, but the issue is clearly NOT on bobs end.

Thank you for looking into it, Pez.

Yes a few of my mods are disabled and I have a few setting tweeked also I did mess around with angels mods enabling and disabling too. And that just broke things. Vut it looks like you fixed things

Yeah, the comment from the other end is to comment out line 7 for now, an actual bobs/angels integration is on his to-do list, which may be a while away.