BuildCraft version: 7.99.17
Forge version: 14.23.4.2725
Singleplayer or multiplayer: Singleplayer, but likely persists in multiplayer
Steps to reproduce:
Create a crafttweaker script with the lines

recipes.remove(<buildcraftsilicon:assembly_table>);
recipes.remove(<buildcraftbuilders:quarry>);
recipes.remove(<buildcraftsilicon:laser>);
recipes.remove(<buildcraftfactory:autoworkbench_item>);

Launch game

Assembly Table and quarry retain their recipes while the laser and autoworkbench lose theirs

Additional information: There may be more recipes with this issue, but these are the few that I've tested so far.