Position Correction Using a TM PosInput 2

I would like to ask for some more help. How would I correct an incremental encoder position in motion(during a move) as it passes through known absolute positions that have a digital trigger?. The encoder is known to lose counts as it is an external encoder. So now I would like to correct the position when it is moving (or in motion as it passes through known physical mechanical positions). Is that at all possible?. If so, kindly help me on how to do so. If not, what is the best way of correcting the position. I am using a TM PosInput 2 for my position detection. If there is an example, kindly help me with that as well.

Your help will be greatly appreciated.