Yup. It's less convenient than uploading your config, but since you already know how to reconfigure everything, you should be good to go.
This experience, plus what I've read from others, makes me nervous to switch to SCALE. I'm sticking with Core for as long as possible.
I'm 99% sure you dealt with a corrupt (or invalid syntax) config file and it threw off the SCALE middelware/GUI. (Truthfully, the middleware shouldn't conk out like that, and should have fallen back to some sort of safeguard, rather than imprisoning you in a state of limbo.)
The command-line (terminal, SSH, etc) is always more accurate than the GUI. So lesson learned: if you want to know if your pool and data is still safe and intact, the terminal is a good bet if the GUI seems to be lying to you.