> In C they use these st loader files which is fine

ST's tools should work for flashing Rust firmwares too, they take elf or hex files and they don't care what language they're compiled from

> but do I need to re-flash my bootloader every time

probably not, if the thing you flash only contains data for the external flash the internal one should stay unchanged. that's what probe-rs does at least, but the ST tools probably do too