After getting on to play for the first time after the new update I noticed alot of my old raw science purchases gave been removed. Namely all of my scab scanner upgrades (other scabs and especially the raw science upgrade), my acorn shovel upgrade (which actually didn't work anyway), and the sign bundle that I bought. Not sure why these were removed but I would hope I could get them restored. 

The most likely got removed because the cost to purchase a lot of items in the shop changed, and that somehow put them back in the shop, regardless of if you bought them pre-update or not, the only noticeable affects are that my raw science and scab scanner were both removed so I'll have to re-purchase them at their inflated price.