omg I figured it out.
The switch I was using to enter into bootsel mode isnt actually connected to the bootsel pin.
The original firmware must have its own logic on boot for triggering bootsel mode when a certain switch is held.
Thats why when I flashed my own firmware that switch stopped working.

The real bootsel pin is connected to that footprint labelled "boot" in your screenshot.
Once I shorted that with a wire (the switch is unpopulated) it successfully booted into bootsel mode.

It was a bit of a silly mistake but I learnt a lot from everyone's advice. Thankyou