My last 2 Superjets had this same problem. From the factory, the foam filler holes are only covered by stickers. This, mixed with the other areas that aren't sealed up properly mean that water WILL get in there eventually. When you leave your ski in the sun, the water/foam heats up, evaporates and cools down, sucking the sides in. It's kind of like leaving your fuel can in the sun and letting it cool down.
Anyway, if you refoam, make sure all the inside is nice and dry and foam free, and leave it for a couple of days (preferably in the sun). The sides will eventually get thier correct shape back (maybe not dead straight though), even more so when you pour your expanding foam.
It's worked for the last 2 that had extremely sunken sides anyway!