Question:
If I have a meter, where the one phase CT was connected in reverse, is there a way to change that in PNPScada to a positive and then to show the recalculated data?

Answer:
If the meter has the additional data somewhere. If not, you can't. Pnpscada cannot create data out of nothing.

For example, today I had a case with an A1140 where it seems the Energy is vectorially summated before forwards or reverse energy is logged in the Energy Register, which means the data is lost.

What some suppliers do for customers that trip some phases to tamper is they multiply the profile before billing, but that is an estimation algorithm.
You can also read the meter with the meter manufacturers software, like Elster's PMU, to get the data that you need.