Jb4 is plug and play. You can disable it before going into the dealer or remove it. Charge pipe shouldnt be a problem since it upgrades the plastic piece. Downpipe shouldn't matter if you're bringing it in for an oil change, and should not affect warranty.
Was - 08' E90 328i|Sparkling Graphite Metallic|AA Tune|Steptronic|Navigation|Comfort Access|Sport|Matte Black Kidneys
Now - 11' E90 335i Performance Edition|Space Gray Metallic|Sport|Premium|Navigation|Steptronic|JB4|E R Charge Pipe|HP Autowerks Foam Filter