I hope you had the original owner of the trigger(s) sign on and remove the triggers. The triggers stay with the account that set them.
Autocrat will not process a row that has anything in the status column (4th column added).
Unless you changed more than the merge job, everything should work the same.
Is the merge written on the Form Responses sheet?
Does the columns added by Autocrat line up with the correct row?
It seems strange that a merge would start failing if all that was changed was the person setting the trigger.