Ran into the same issue so I created a quick solution to solve the problem temporarily until I can rely on the native gui.App.clearCache function. This removes the entire Cache directory and recreates it asynchronously.
This requires fs-extra and should work on Linux, OSX and Windows.
var customClearCache = function(){ var dir = path.join(gui.App.dataPath, '/Cache'); fs.remove(dir, function(err) { if (err) return console.error(err) fs.mkdirs(dir, function(err) { if (err) return console.error(err) // This is where I start my app }); });};