Apparently this bug was present on the test server as well. Per someone else's comment, it was a) reporter, and b) forum mods stated that they forwarded the bug report to the devs. They didn't fix it and so blue mods that were either a) slotted into an item or, b) in your stash got scrambled. The presumption is because they added new blue mods that they screwed up their database tables.
In order to avoid this bug you would have had to have known about it from the PTS, assumed that they wouldn't fix it, and then moved all blue mods out of your stash and removed from your gear before the patch occurred.
I have no expectation of Massive fixing this issue and instead telling us that "re-earning our god-rolled blue mods will give us a sense of Pride and Accomplishment".
This has happened to a lot of folks. In my case some mods have been replaced. I now have two god-rolled bleed resist mods but other mods I had are gone. I am thankful that my red crit mods were left untouched, because on the PTS those were the ones that disappeared, but still it's kind of disturbing that this bug was a known bug that made it live.
Here's a Player Support thread I started that has an Ubi response if you want to add your info to the thread:
https://forums.ubisoft.com/showthrea...d-by-New-Patch