I use containers too. I didn't loose any data after I enabled dev mode and added the extension back. Perhaps you removed the existing extension first and lost data that way?
It's odd - on my laptops, my multi-container settings were preserved, but I opened firefox on my desktop last night and they had vanished. I did not remove any add-ons myself.
Only difference is that I restarted the desktop Firefox and also enabled Shield studies to get the temporary fix. On the laptop I just upgraded to 66.0.4 and only then restarted it.
To the best of my understanding, here's what happens.
* containers.json is reset to default
* if you have any non-default containers, they are lost
* the underlying data is still in IndexDB (??) but isn't connected to the custom containers that were wiped out
* if you're clever and can read the IndexDB (or wherever the data is, it's moved a few times) then you could probably rebuild your containers.json file
