First, please check if you can see the missing DLCs in your "Manage My DLC" menu. You can access this menu if you go to the Steam page of Pinball FX3 -  you can find this option on the right side of the page.

If you see your DLC, please try to enable them again with first removing then putting back the checkmark.

If you still experience problems with the transfer of tables on Steam, please use the ‘New Support Ticket’ option above.