I have two examples and I'm not sure if they qualify for Best Partial Redesign or Atrocious Partial Redesign...
The first is Bucks County Country Club in Jamison, PA, where the addition of housing to a circa 1961 William and David Gordon design necessitated the creation of 5 new holes, which were done by a fellow named Jeff Broadbelt. The new holes, even though they occupied some trying pieces of property, were all quite daring architecturally, with one absolutely fabulous long, uphill par three to an amazing green being the highlight.
Although the replacement holes mostly worked well, they only served to highlight how mostly mundane, rote, and unimaginative the original holes were and the course now comes off like a hot, frilly pink negligeee sewn onto a pair of thick women's corduroys.
The second example is Cobb's Creek. In the mid 1950s, approximately 15-18% of the course was co-opted by the US Army for a Nike Missile Battery.
This forced a re-routing by course officials that managed to use all of the existing original greens in new and generally creative ways given the constraints of the situation. That today's course is still fairly well-regarded architecturally attests to that.
However, the net effect is that six of the very best original holes were either eliminated or otherwise compromised and a fair, objective assessment is that each was far superior to the holes they were replaced with.