Flashing replaces the bootloader

make flash writes to offset 0x0, which is where the ESP-IDF bootloader lives. After this the board runs only this image. Any ESP-IDF app that was on the board is gone with it, and won't come back until you reflash that project with idf.py flash, which rewrites the bootloader, the partition table, and the app together.

If the board doesn't respond, hold BOOT, tap RST (or replug), release BOOT to force download mode. The single USB-C port is USB-Serial-JTAG, so there's no auto-reset circuit doing it for you.