The simple answer to this question is yes, your marks are likely to improve if you apply for challenge evaluation in AKTU. 

This answer is based on the experience of my brother who got a back in of the subjects. Initially, he thought of applying for challenge evaluation, but later changed his mind and went for carryover paper (INR 1000). But unfortunately, he got back into the same situation again. This disheartened him and he decided to apply for challenge evaluation (INR 2500) in AKTU. He was able to clear his back by gaining marks through challenge evaluation. This incident concluded the following possibilities:

• The professors conduct wrong evaluation 

• Professors intentionally give a lot of backlogs in order to earn money through challenge evaluation.

So don’t waste your money on carryover paper. Simply apply for evaluation.