You did something as this was working prior to 26.3.48, from the changelog
-fixed crafttweaker support

I have 2 simple lines in CT to change the magnetite furnace recipe as my pack has Better with Mods hardcore turned on (which smelts all ores to nuggets).

furnace.remove(<fp:erze:4>);
furnace.addRecipe(<immersiveengineering:metal:29> * 4, <fp:erze:4>);

immersiveengineering:metal:29 is iron nuggets from Immersive Engineering

From CT log

[POSTINITIALIZATION][CLIENT][INFO] Removing furnace recipes for: <fp:erze:4>
[POSTINITIALIZATION][CLIENT][INFO] 0 recipes removed for: <fp:erze:4>
[POSTINITIALIZATION][CLIENT][INFO] Adding furnace recipe for <fp:erze:4>

Magnetite still smelts to 4 iron ingots.

prior to 26.3.48, craft tweaker support did not work at all (at least in 1.12)

Also "furnace" refercs to the vanilla furnace and that is completly handled by craftweaker/minetweaker. I dont think I can to something here :S ( or at least I dont know what)

It did I had that recipe working maybe not on the immediate version before 26.3.48 but certainly on older ones.

Yeah it's the vanilla furnace the script isn't working on.

does furnace.remove searches for output of for input ?

Output but that remove line I added in after the furnace recipe change didn't work

it is locking for somehting with fp:erze but cant find something. In game the recipe is still present and working ?

I dont add a recipe wich outputs magnetide, I only add a recipe to add smelt magnetide to 4 iron, and if remove is searching for output I think chaning the search pattern to iron should remove my recipe (propaply also others)

In game fp:erze:4 (magnetite ore) is still smelting to 4 iron ingots which is default for FP.

The script is supposed to change that to 4 iron nuggets.

The script does nothing and magnetite remains smelting to 4 iron ingots.

I can't find any errors in any log pertaining to the script entry, it simply is ignored and does nothing.

Please ignore furnace.remove(<fp:erze:4>); I added that afterwards which is wrong I know, the 2nd line is supposed to change the furnace recipe.

I dont know much about Minetweaker, have you already asked someone who is familiar with the scipts ?

Ok sorry for wasting your time, the behaviour of CT has obviously changed between versions.

Remove magnetite ore to 4 iron ingots smelting recipe
furnace.remove(<ore:ingotIron>, <fp:erze:4>);
furnace.addRecipe(<immersiveengineering:metal:29> * 4, <fp:erze:4>);

Works fine before I didn't need to remove the old recipe, the previous script was

Remove magnetite ore to 4 iron ingots smelting recipe
furnace.addRecipe(<immersiveengineering:metal:29> * 4, <fp:erze:4>);

Obv something changed between CT versions and removing is now necessary.

Again sorry for wasting your time.