After flashing firmware that requires an updated system firmware to an Electron that is part of a product, the cloud starts updating system firmware with something called “safe-mode-updater”.
This is a really cool tool for updating electrons!
Is it possible to use this for Electrons that are not part of a product?
It currently isn’t implemented for non-products, but you can flash the system parts manually OTA. It might get implemented some time in the future, but no guarantees on that one 
In case someone else comes here looking for something similar, feel free to use: https://github.com/hwestbrook/particle-device-healer
Disclaimer: this is only lightly tested and will use a ton of data if you either update a bunch of devices or encounter some bug I have not foreseen. Use at your own risk!
On another note, all the data provided from safe mode is pretty interesting.