You do understand that there is literally no point in making such tool?
The moment ID becomes "nullified" game automatically assumes that given blocks are now AIR, they just stay in world data until you load it.
It's cleaning itself. The only viable approach to such things.
Only valid argument here would be lack of free IDs for new mods - which is ridiculous, I can't imagine any map having that much stuff.
Sure you can remove IDs, load tons of world data files (which is IO that takes time), then iterate over chunks and then blocks and then check agains every removed ID and then change data and save it back. Oh and did I mentiont TileEntities and Entities saved in world? How about Any other mechanism that every saved anything block-related? How about other mods? You can't even be sure you removed everything - and then BAM! Other mod suddenly loads different blocks from it's modded backpack items.
Not only pointless, but close to impossible.
Why bother?