Worry NOT my friends. Your warranty is unharmed by properly servicing your knife.
https://www.spyderco.com/service-support/warranty-repair/
✓ Spyderco’s knives are assembled to exacting tolerances by trained technicians, so we discourage end users from disassembling or adjusting our knives. If a knife has been disassembled and reassembled correctly—so as to maintain its proper mechanical function—this warranty remains in full effect. However, if a knife has been disassembled and reassembled in such a way that, in Spyderco’s sole determination, the proper mechanical function of the knife has been compromised, it is no longer covered by warranty.
If you are going to apply a patina to the blade tang you should seal the face of the tang that makes contact with the PB bushings,inside the pivot hole, the detent ball track and the compression lock face. I use a Silver Sharpie. Its more like a paint than an ink and works pretty well for keeping the patina away from where you don't want it. Don't forget to soak the tang in alcohol and clean the paint off before reassembly.
I would also suggest polishing down the factory grind lines down to like a 220 grit satin. This allows your patina to coat the blade more smoothly and the reduces the roughness of the surface where red/rust can grow but leaves just enough surface texture to retain the gray, brown and black rust you want. Once you have a nice dark gray, brown and black patina, you'll need to seal the surface with oil. Massage it into the patina, just like you're spit shining shoes. You know it's coated well when your finger leaves streaks in the viscous coat without pulling oil from the blade onto your finger.