This happened to me after many hours of successful compilation, flashing, and troubleshooting on the local cloud. Something happened and my photons would no longer accept OTA updates. I tried flashing my binaries over USB, which worked, but those binaries would only run in safe mode. However photon-tinker.bin in particle-cli/binaries would flash and run properly both OTA and with USB.
I was able to use this solution to recover. Due to my setup, my compilation host is unable to connect to photons with USB, so I used the advice from @peekay123 to compile. Then I copied the binary artifacts to a machine that can connect with USB, and used the steps: