Hello Dafnis, I recently posted a somewhat similar question. In our case, the variables are still in our app, but the definitions of the variables are lost. Did you ever learn more about the issue you encountered?
I've a similar issue here. I've dashboards created with 3.1 desktop and published on a 3.1 server and all works great. Now I've been forced to upgrade desktop to 3.1.4 since 3.1 has expired.
If I take that dashboard and simply reload data, when publishing it on the server all the variables that were created from the variables overview on the bottom left corner of the screen are missed!
I guess there's an incompatibility issue between above versions. If true I'll be forced to upgrade server platform to 3.1.4 and I think it's not a good thing to force users upgrade a server platform due to a desktop tool forced upgrade. Maybe it'll be nice that Qlik reconsider this nonsense policy...