ThomasOeser If in last HCW run CMT was enabled, HCW doesn't detect this and put a checkmark in "Enable Centralized Mail Transport".
But if you only change mail transport certificate and unselect CMT in the new Hybrid Wizard it will not disable CMT, it will preserve the existing mail flow configuration. So, you don't need to always put a checkmark in "Enable Centralized Mail Transport" every time you run the HCW. In fact, we want customers to choose only those configurations which needs a change and deselect anything that doesn't need a change.
VikBh705 we will take a look into this. Although it doesn't change anything configuration wise, but HCW is just resetting the feature list to last run selected options. We will double check this, if it can cause issues. To disable CMT, you just need to select all 4 connectors and deselect CMT, that should do the trick.