I have this same issue while flashing my HKPilot32 board (Hobbyking Pixhawk).
Usually, I should use
make px4fmu-v2_default upload to build and upload PX4 firmware for HKPilot32 (https://dev.px4.io/en/setup/building_px4.html), however, I'm having the following output:
[1/1] uploading /home/arpac/src/firmwa...x4fmu-v2_default/px4fmu-v2_default.px4
Loaded firmware for 9,0, size: 1021841 bytes, waiting for the bootloader...
If the board does not respond within 1-2 seconds, unplug and re-plug the USB connector.
Found board 9,0 bootloader rev 5 on /dev/serial/by-id/usb-3D_Robotics_PX4_BL_FMU_v2.x_0-if00
ERROR: Board can accept larger flash images (2080768 bytes) than board config (1032192 bytes). Please use the correct board configuration to avoid lacking critical functionality.
Nonetheless, flashing it with
make px4fmu-v3_default seems to work fine for now.
Someone has the same issue or knows a workaround for it, please. Thanks.