I don't know if this is due to a server crash (when was the last one?) but I figured I'd mention it just this winds up being a bug.
A few hours ago, probably around 7 or 8 PM EST, I decided to organize a bunch of packs I have. I lined them up in a neat row and distributed tools and materials amongst them to make things easier to find (a pretty excruciating experience due to the bag closing bug). It probably took me 20-30 minutes to do.
I log back on hours later and discover that my bags are back in their original positions and all the items I sorted are back where they were.
Now if the server crashed sometime shortly after I did all that then I guess that's that. Gotta deal with it. But if it didn't, or it was shut down in a controlled manner, then it sounds like there is an issue with this information being saved properly.
I've heard plenty of other people complaining in chat about bags being empty that were full before or missing items. Of course some of this could be blamed on people taking stuff or whatever but I know in my case the fact that the bags were back in their original positions (a pretty distinct layout) tells me it was some sort of server rollback or data loss.