Good question. Let's look at the PFS FAQ to see what it says.
PFS FAQ wrote:
What are the rules for upgrading weapons, armor, and wondrous items?
You may upgrade one weapon, armor, or wondrous item to another as long as the new item occupies the same slot, is made of the same material, has the same general shape, and has all of the abilities of the original item.
I left out the rest because it's all just examples.
They definitely both use the same slot, they're both "slippers" ("general shape") and neither item says what material they're made out of, so those three requirements are definitely satisfied. The only thing that's even slightly questionable is whether the fact you spend the Spider Climbing slippers in 1-minute increments, while the Scampering slippers in 1-round increments; you could argue that since you have to spend the Spider Climbing in larger increments, it doesn't have "all of the abilities" of the Scampering slippers.
That's just hypothetical; I don't think you'll actually find anyone that will argue that the limitation counts as an "ability". You should be safe to do the upgrade; just tell your GM what you're doing (like you're already supposed to do), including what the difference between the items is.
