The schematic shows pin 2 of P3 to be connected to VIN.  This is surely a mistake?  It should be the target voltage, i.e 3.3v, not the supply voltage.

If the board is powered from USB, VIN is 5v so an attached ISP programmer will drive the SPI lines at 5v and probably damage the RFM69 and Flash SPI memory

Hello Jsole,

Any pin marked as VIN in the board is not directly connected to the 3.3V rails, it goes through an LDO to make sure the supplied voltage is 3.3V to the 3V3 rail.

Saying that, make sure the ISP programmer I/O levels are 3.3V. You can use an ISP that offers 5V/3.3V selection, like this: https://core-electronics.com.au/usbasp- ... ammer.html. Alternatively, if you only have a 5V ISP you can use/build a simple lever converter for the SPI lines.