If you alter a gun to make it fit your needs while having the work down first class you should not hurt the gun value too much. Opening chokes to make the gun versatile and useful is no sin in my book. Cutting the barrels is a sin, you might as well port the barrels and ream the chambers to 3" with long forcing cones.

Most refinishing is done to keep a nice gun looking like a less worn gun. No sin but not going to improve value to any collector. When over done it does decrease the value to many knowledgeable buyers. It almost certain that you will never recover your investment in a total refinish job so do so only for your own enjoyment and let the next owner figure it out after you are dead.