swapping files using (magic files ) issue UR10

ladd

We had a robot to change out on our line both are ur 10 first robot had an elbow joint issue so decided to change out complete robot ,4 bolts a connector and file changes to complete thinking it would be faster.....not,,. we didn't want to un-wire controller (hard wired in) , UR 1 controller type  cb3.0 UR 2 controller type cb  3.1 .....so robot 2 was swapped to a controller cb3.0 and we did the magic files and followed the  instructions  ... seemed to be ok at first  but issues arose 1. takes for ever now to boot up 2.if protective stopped on restart screen will freeze sometimes will just die and have to restart robot 
Has anyone had this issue after swapping robot to different controller  .. we did move the dongal with each robot  i have swapped other brands of robots out like this but not seen this issue