There is a protection diode that prevents power from Vin to USB, so your USB port is safe.
If you want to protect your Vin source against USB power, you’d have to add an external diode too.
But I thought there was something in the docs about this and there are several threads in this forum too (mainly about the Core, but the Photon behaves just the same in this regard).
See Vin pin description here
https://docs.particle.io/datasheets/photon-datasheet/#pin-description
https://docs.particle.io/datasheets/photon-datasheet/#power
The key info is the bit about “a reverse polarity protection series schottky diode between VUSB and VIN”
Forum discussions
What happens if both vin and USB are connected to 5V
Use USB serial for datalog while core is powered over Vin?