Delete app data without deleting app
Depending on the version of iTunes you have you may be able to do this. You need the last one that has App Management built in. This one to be specific.
As long as the needed app is listed in iTunes and you can find the .ipa file on your hard drive, it should be safe to delete the app from your phone and then sync with iTunes to put it back.
It has been a long time since I tried this, you might want to wait till someone else who has done this more recently can verify this just to be safe