Hello Ilkay,
Thank you for your inquiry.
J-Link will only reprogram memory sections that have changed. So make sure that your debug build does not generate any code for 0x08000000 - 0x08003FFF.
Could you provide us with a J-Link log file when that happens?
https://wiki.segger.com/Enable_J-Link_log_file
Would it be possible for you to send us an example project where this issue is reproducible?
Best regards,
Nino