If your cheque book or cheque leaves was/were taken without your knowledge, whether they were blank cheques with or without signature or fully made our cheque it is a case of theft you should or should have done the following: (1) Immeditely inform your bank about the loss of the cheque book or cheque leaves with numbers and give stop cheque instructions.(2) more importantly you should file FIR with the police. If you had done these things you can easily explain under Section 139 if the party goes to court. If at the time of filing FIR you were not knowing who the thief was, you will know it when you receive the demand notice under Section:138. Immediately you can give the name/s to the police. If any of the cheque leaves had been encashed police can trace the thief through the bank transactions. With a stolen cheque a thief may withdraw money. He will not be foolish enough to expose himself through Section 138.
As all the above safeguards are available one suspects somehting is wrong somewhere.