IF you had stuff in your player inventory when leaving the A8 game and then starting A9 this MIGHT happen i am afraid as the Toolbar/Player Inventories have been reworked and we could not "save" the previous state. Same applies for fridges, constructors, furnace and deconstructor as those now all have a different way of setting up their inventory.
If you start a FRESH A9 game (or if the vanished items relate to any other container), items vanishing from the toolbar/inventory should NOT happen. In this case > please file a bug report. Thx.