R1v3r, that happens all the time. It happened to me at least three times and I have seen dozens of users reporting the same on TJC. For me it's usually downloading a bunch of files in Sailfish Browser that does it. A "problem with registry" system popup and the next thing you know, all your Weather locations are gone and so are most of your Warehouse repositories and sometimes SMS messages and emails or whole email accounts. How are those things related to file operations and each other? I have NFC.

The only solution as far as I know is to put them back manually. I would love to hear otherwise.

One word of advice, at least according to my personal experience. If you have Sailfish Utilities installed, do not get tempted to rebuild app registry! That will make things only worse.