You exported the layouts from system A and tried to import on system B and found that the selections of Custom Reports on system B were overwritten.
SAP Hybris Cloud For Customer
Selections of Custom Reports are not supported via Content Transfer.
You will need to maintain the selections for Custom Reports once again after performing Content Transfer.
Custom Reports, Report Selection, Import, Content Transfer , KBA , AP-RC-UIF-FLX , Page Layout & Key User Configuration , Problem