The default toolchain_program() for https://github.com/amaranth-lang/amaranth-boards/blob/main/amaranth_boards/tang_nano_9k.py uses openFPGALoader.
It lacks the "-f" option that writes to flash, so only programs the RAM. If you want persistent FPGA programming you need the "-f" option.
Not sure how this should be handled. Is there a way of adding programmer options, eg via the environment?