Parallel proceedings civil and 138 of ni act

There are two aspects to the matter. Recovery of money is under Civil Liability where if the case is settled ie. judgment is received does not affect the case under Section 138 for Criminal proceedings and may be pursued to its logical end.

You can very well proceed for recovery of the money under the Judgement received in your favor for recovery of the money.

In response to your query, 

NI Act case is no maintainable U/s 40 of the Indian evidence Act, 

Because, according to Section 10 of CPC- No Court shall proceed with the trial of any suit in which the matter in issue is also directly and substantially in issue in a previously instituted suit between the same parties, or between parties under whom they or any of them claim to be litigating under the same title, where such suit is pending in the same or any other Court in India with jurisdiction to grant the relief claimed, or in any Court established or continued by the Central Government beyond the limits of India.

Regards,

Aryan Raj