TBH, I am still not sure they are actually being deleted, destroyed, whatever. I feel like its just to get the best showing out of the people.
In the first tournament they had, the super dragonballs were on the line, which were used to give the losing universe something anyways, they had a reason to go all out even if it wasn't a great reason. So, to make them try even harder, they put their "existence" on the line, or so they told them, this could very well not be the case because it seems to almost always never end up mattering.