To clear up what is happening here is the how and why:
If you have two or more of the same "can only have one" item, you were targeted by a script. If your char did not have two "can only have one" items at the same time you were not targeted by the script, this means any alt you have not played after the merge is safe.
The people targeted by the script are some exploiters but probable more people that just do some things regulary.
For example many people to save inventory space claim the totem of origins when they need to use it, before if you had the totem already you did not get it, now you get a second and is therefore a target.
Another ting is if you are running Isle of Iron statues, finishing hardmode you can get the mystical dust in the hardmode chest, before you would just not pick up the dust when you had one in the Inventory, now you can pick up a second and will be a target.
Then there are the milestone symbols, before you did not get them if you had it in the inventory, now you can and therefor is a target.
Probable also many more ways to get two "can only have one" items without you really knowing of it.
So this script was run on tuesday this week around 18:00 GMT i would guess(+/- a few hours). And everyone that was in the target group at that time were stripped of all their "can only have one" items. As far as we know the script was never ran before that, and hopefully will not run again in the future.
It was never a problem with the bags, this was only poor troubleshooting that brought the bags into the picture.
But some bags are "can only have one" items(dont make sense, but it is that way), so if you fear you were in the target group you cannot just check if you have the bag or not. What you can do, is check if you have an item that is "can only have one" in your Inventory. If you have just one "can only have one" item you can be sure you were not in the target group.
There is one exception here, the milestones quest reward ring used to be "can only have one" but that was removed, but the older rings are still marked "can only have one" even if they are not to the system. This ring will not be removed by the script.
If you lost your "can only have one" bag, among them being the veteran bag and money-shop bags, you have not lost the items that are now hidden, as soon as you get the new bag all the normal items that was beyond the first 24 slots of your inventory will still be there.