For example mod adds non solid ore and it replace smooth stone in your redstone machinery making it fail. Even Mojang doesn't care about it, so why modders should?
Hm I assumed if you left that area alone it will leave the IDs
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Yeah I realise but it should only save the chunks it edited, even then it should leave data values untouchedloading with MC edit is loading all the chunks.
I was talking about regenerating ores, not generating weird pseudo ores. I don't really understand how these pseudo ores would work. For example let say that you want to add redpower to the world that didn't have it before. So if you wan't to just replace block ids, you would have to have block with 7 different metadata types generating with on very different levels with different cluster size and frequencies. Some mods also add more complicated generation. Railcraft saltpeter generates in hot arid biomes with sand and sulfur generates in extreme hills near lava lakes. So practically you would have to replace those pregenerated pseudoores with different blocks, it really isn't that much different then just generating in smoothstone, except that it would make it a lot more complicated.
It feels like a year from now, we'll be digging deep in the earth just to find the elusive vein of cobblestone.