Far as I know, all you can do is replace the "tape" (stickers) since they apply right to the door frame. The old tape has to be removed before applying the new. For the front doors, parts #5 and #6 (for each side).
Pillars on the Gen 3 CR-V are the painted metal door itself. You have to remove and replace the stickers/trim/garnish.
After a ton of searching for the best method to correct or replace pillar trim, I ended up removing and replacing with the factory garnish from Honda. The job is a major pain and would only be easier if you were willing to replace all the metal chrome trim as well which is expensive.
I detailed the process as best I could in this post including part numbers and tools for the job:
The following relates to my Gen 3 2011 CR-V SE. There may be similarities to other years and models. There are threads on here talking about the black treatment on the B and C pillars fading and cracking, but not a lot of concise directions on how to fix it. It is called pillar garnish, tape...
If you have any questions not answered in that thread, ask them and I'll see if I can provide additional information.