Combining a tool with an enchanted book should add the enchant onto the item.
When clicking on the output item of the anvil it destroys the item.
Steps to Reproduce:
1. put any tool into the anvil
2. put a book into the anvil to combine
3. try to obtain output item
4. poof item gone
Thank you for your report.
However, your ticket has been resolved as a duplicate.
This issue has been linked to the original bugreport: MC-91521. You can find or add further information on that report.
Please search before reporting any bugs, as it's likely that one exists already.