I was just wondering if there's a huge difference between these two preparatory methods? My huge two ball arsenal used to be hit with Abralon pads about once every month or so, and this time around the pro-shop dude didn't have any, so he used wet sand paper. Anybody have any experiences with this?

While there is no bottom line, theoretical difference between the two (1000 grit is 1000 grit), there is a practical difference in that Abralon with their attached foam pads are easier to use on round balls. You really should use either a CAB (contour abrasion block) or a damp sponge to back wet/dry sandpaper, to help the abrasive conform to the surface being sanded.

The other thing that you should do that many people do not is keep a close eye/hand on the abrasion material, no matter what it is. When it's no longer the grit that claims to be (the abrasive material has either gone away or has broken down into smaller piece), you must change and throw away the old piece.
I'd bet that most people's balls using 1000 grit Abralon are much closer to 1500 or 2000 grit because the pad has gone much smoother with wear.

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"None are so blind as those who will not see."