Mods became uninstalled and lost their rules.

[PiersAS]

I have a skyrim modlist with around 1200 mods. Somehow I managed to break it.

At some point, I think I did a purge and deploy. Then I got a series of error messages that I did not understand like files had changed outside vortex, and such. 

Anyway, now all the mods have become uninstalled and have lost their rules. Probably take a day or two to add them back.

So what did I do wrong, can I fix it by getting back the rule information and how do I prevent it from happening again?

I'll make a point to use collections to save my work online from now on.