S3D will let you rebuild with new IDs, the trouble is that you then need to test with every other mod you are using to make sure you haven't broken anything. Best might be a CTD, since you'll know it is broken, but it is also possible to break things so that something just doesn't work, which is considerably harder to notice.
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"Government, even in its best state, is but a necessary evil; in its worst state, an intolerable one." — Thomas Paine
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