In reactions_standard.txt, there may be a section more or less like this:
[REACTION:ALL_ECONOMIC_ENTRY]
[NAME:make all stones economic]
[SMELTER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SANDSTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SILTSTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MUDSTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SHALE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CLAYSTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ROCK_SALT]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:LIMESTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CONGLOMERATE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:DOLOMITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:FLINT]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CHERT]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CHALK]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GRANITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:DIORITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GABBRO]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:RHYOLITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:BASALT]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ANDESITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:FELSITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:OBSIDIAN]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:QUARTZITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SLATE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PHYLLITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SCHIST]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GNEISS]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MARBLE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:HEMATITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:LIMONITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MAGNETITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GARNIERITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GOLD]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SILVER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:COPPER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MALACHITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GALENA]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SPHALERITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CASSITERITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PLATINUM]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:TETRAHEDRITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:BISMUTHINITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ALUMINUM]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:KIMBERLITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:BAUXITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CINNABAR]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:COBALTITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GYPSUM]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:TALC]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:JET]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PUDDINGSTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PETRIFIED_WOOD]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:GRAPHITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:BRIMSTONE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:REALGAR]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ORPIMENT]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:STIBNITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MARCASITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SYLVITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CRYOLITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PERICLASE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ILMENITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:RUTILE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CHROMITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PYROLUSITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:PITCHBLENDE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:BORAX]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:OLIVINE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:HORNBLENDE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:KAOLINITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SERPENTINE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ORTHOCLASE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MICROCLINE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:MICA]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:CALCITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SALTPETER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ALABASTER]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SELENITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:SATINSPAR]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ANHYDRITE]
[REAGENT:1:STONE:NO_SUBTYPE:STONE:ALUNITE]
[PRODUCT:100:1:BAR:NO_SUBTYPE:METAL:ADAMANTINE]
[FUEL]
If it is there, try removing all the reagent lines, temporarily. Doing so was toggling my oceans back and forth between good and evil, some weeks ago. I posted a question about it but no one seemed to know why so I stopped worrying about it. It might work for you. If it does, the evil places will stay when you put the lines back, once the world is made.
Edit: If you don't use that reaction, try adding it. That might work the same way.