I have solved my problem so far.
My assumption was that the connection issue had to do with the reset of the board and that it may had something to do with the way the reset is carried out maybe related to the bootloader. I thought that the bootloader on it was a standard Arduino bootloader since the board is based on a Arduino design but it seems not to be the case.
My printer is a Wanhao Duplicator 4 which is based on a variation of the mightyboard somewhere between rev E and rev G/H and it uses a special bootloader-mightyboard which the rep2/2x apparently also uses.
It turns out @dockterj has done a lot of work to get the replicator 2/2X to work which Wanhao Duplicator 4/4x printers can also benefit from. I came across this post How to connect klipper to Makerbot Replicator 2X？ - #34 by dockterj where it is mentioned that @dockterj had implemented an additional reset method restart_method: mightyboard I tried to change to his klipper fork GitHub - dockterj/klipper: Adding support for MakerBot Replicator 2 and using his alternative reset method and this solved the problem 
Thank you @Sineos for you suggestions which kept me trying to find a solution and to @dockterj for your great mightyboard work. I hope you’ll get it into the main line soon
I know that @Imesh_99 probably haven’t got a solution to his problem and won’ be able to use mine since he has a BTT board. So even though my problem is solved, the thread shouldn’t be make as solved.
Regards
Esben