1. It shall be presumed as per law, unless the contrary is proved, that the holder of a cheque received the cheque, of the nature referred to in section 138, for the discharge, in whole or in part, of any debt or other liability, so your friend will have to prove his liability before the court as to to how he had borrowed you the said amount.
2. It wouldn't affect your job as cases under the negotiable instruments Act of of quasi criminal nature only.
3. You have a good prima facie case but case needs to be contested deligently by an efficient advocate.
4. court will consider the fact that the other person has no source of income as well as he would not be able to show any transactions showing that he had given you any money. Also, you can file in application before the court to send the cheques for forensics examinations as well to prove your claim.