Hello Alice,
Thank you for your attention first.
I realized after the first post, as settings are attached I can successfully debug from ram without using Flash.
While designing my board I referenced the LPC-Link2_v3_RevB.sch. Did you check my schematic? W25Q80BVSSIG, which is also on LPC-link2, is used as an external flash but it is connected from jumpers, that's the reason why it's not seen in the schematic. When I try programming external flash via GUI Flash Tool, it can recognize it but it gives a time-out error.
So, If I can debug on ram, what could be the problem with flash? As I said, it recognizes the flash, so it doesn't sound like to me there is a connection error with the flash.