The warranty covers defects.
TLDR: they'll fix it up and it probably won't cost you a thing except for postage but please clean it up before you send it.
Longer version, for anyone else interested : They will usually clean up, replace missing/damaged tool springs, replace liners and scales (unless you have special scales and don't want them replaced), reshape and/or repolish your blades, replace missing/damaged scale tools and oil the knife... Usually for free but they might make you pay a small amount for the scales (alox scales in particular) and for minor missing tools (bits, corkscrew screwdriver).
That's why I usually clean a knife as best I can before I send it to them, out of respect and also hoping they'll spend more time on other tasks if I do that one myself.
They will also replace any broken tools but will always (in my experience) make you pay for them. It's always a tiny amount though. The most I've ever paid after the SPA treatments was CHF 15.- for an Alox knife for which they replaced about 85% of the parts. (keep in mind I didn't have to pay for postage since I brought it to a flagship store)
If you have a broken tool (snapped blade for example) and special scales, they will warn you that they need to remove the scales to dismantle the knife in order to change the tool and can't guarantee that the scales won't be damaged. If you're not willing to take the risk to lose the scales then tell them. They usually communicate very well and you can ask for a quote ahead of any work being done if you're worried it might cost you too much.
If you have scales in special materials (eg wood handles from a 1890 soldier's knife, or the later fiber ones) that you want/need replaced, they can custom-make them but it will generally cost you between $50 and $90. And you'll denature the oldness of your knife. Also, no ebony, can't remember what they use instead now.