I guess WebStorm is not the problem. It does not delete any files - but if course it has to change some of its files, when your testing period is over.
You could use NetBeans or Eclipse instead. But there's no solution which is as fast, lightwight and well-working like WebStorm (and other IntelliJ IDEA derivates like PHPStorm, PyCharm, AppCode etc.).
I tried many alternatives and worked with different IDEs before. For me, WebStorm is the perfect choice. It starts by 5.90€ per month for an individual person - it's just a question of personal priorities.