Hi Kopone,
You could try to use sequence of debugger commands below placed into *_Postload.cmd command file.
Each time a code is loaded into MCU this script is executed. This cmd file is usually located here:
{Project directory}\cmd\CFV1_BDM_P&E_Multilink_CyclonePro_Postload.cmd
// After load the commands written below will be executed
flash
flash select 0
flash arm
srec MyData.s19 // replace "MyData.s19" by your s-record
flash disarm
flash unselect
reset
Stanish