Your best strategy would be to write your own bootloader.

The existing bootloader receives data through the serial port and writes it, a page at a time, to the flash. Your custom bootloader, instead, would receive the data through the nRF module and write it to flash, a page at a time.

You could use the source code for the existing bootloader (maybe use optiboot?) as a starting point and remove the UART code, replacing it with nRF code.

Of course, you still need a way to enter the bootloader when you want to program it - the easiest way is to ensure that is added into any sketch you upload so you can send an instruction to that sketch to enter the bootloader.

Your best strategy would be to write your own bootloader.

The existing bootloader receives data through the serial port and writes it, a page at a time, to the flash. Your custom bootloader, instead, would receive the data through the nRF module and write it to flash, a page at a time.

You could use the source code for the existing bootloader (maybe use optiboot?) as a starting point and remove the UART code, replacing it with nRF code.

Of course, you still need a way to enter the bootloader when you want to program it - the easiest way is to ensure that is added into any sketch you upload so you can send an instruction to that sketch to enter the bootloader.

You would also need to create a program on the Pi to do the programming over the air - or modify an existing one like avrdude.

It may, in the long run, be simpler to have a pair of other Arduinos (maybe something small like an ATTiny based board) to act as bridges between UART and the nRF modules so they become a transparent wireless serial link.