It's been a while since this post was opened, but I also had this issue recently and recurrently.
After a form including a matrix field has been duplicated, edited and saved, the choice labels are lost sometimes. Actually they are not lost, they are just set to "live = 0" in the DB
Here is the solution
Open your Database (e.g. with sqladmin)
Open the table "ap_element_options"
SELECT * FROM ap_element_options where element_id=[ID of the matix field] and form_id=[Form ID]
Now you should see the table rows with available options (in my case yes, no, Answer C, Answer D) and all are set to "live = 0"
Just edit the fields you want (in my case yes, no) and set "live" from 0 to 1.
Thats it! If you know where to look its solved in 2 minutes.