Hey dudes, I've seen it mentioned in the comments and one other discussion posted in july, I have one temporary fix in case this has happened to you.

How it happens:
1: Place any amount of items in the drivers/front passenger seat
2: Enter the seat that has the items stored on it. Your character will automatically 'shift' the items down into the other open seats. (Usually not the drivers seat)
3: The Luton van is unique in that it's 3rd and 4th passenger seat each use their own storage window; those items will have shifted into the 'vanilla' seat's storage, and not the modded storage, so you're unable to see those items because of it.
4: Not only can you not retrieve the items, it can take you longer to occupy a seat depending on how full it is since you're shifting items around.

How to fix in MP:
1: Have a friend occupy one of the rear storage seats.
2: When you enter the other rear passenger seat, your character will shift the items back towards the front where you can access them again.

How to (probably, sorta) fix in SP:
1: You can probably shift a heavy, throwaway item into those seats to simulate an occupying player (i.e. loading the vanilla seat storage to capacity). You'll be able to retrieve the misplaced items, but you'll still be stuck shifting items around the back seats whenever you switch.
2: If you don't really care for the Luton van itself but really need the items back, you can just dismantle it with a blowtorch. Since it does the same for a glovebox and trunk storage, it's a safe bet that any items still in the car will drop to the ground once it's dismantled.