A little context before I get into the issue. I am building a new multisite with three sites (/, /workshops, /conference). I had permalinks set up across all three sites to be /%category%/%postname%/, and everything has been working flawlessly until today.
I know that you have to set permalinks in the Settings > Permalinks (which will forcibly add /blog before the permalink) and then go Edit it under Network Admin > Sites to remove the “/blog” portion of the URL. Things have been running smoothly for about a month, until today when I had some issues integrating DoubleClick ads. One of the trouble shooting steps is to resave permalinks, so I figured that I could just remove /blog again after attempting to save permalinks. As soon as I did this, literally everything broke. I can barely get anywhere on the site, and get 404 errors everywhere. If I add /blog/category/categoryname manually, then it will find the correct archive page / post about half the time. My next guess is that my Yoast was somehow jacking everything up, so I simply disabled it for the time being and went back and resaved everything (making sure that removing /blog was the last step in the process) but they are still broken, even with Yoast disabled.
Finally, I figured that I would just go grab the “Network Setup” htaccess instructions again, just in case they got corrupted somehow, but still having no luck.
The preview is currently at: http://vb7q-flpc.accessdomain.com/, however I have it currently using the /blog url so I can continue to work on it until I figure this out.