I use a shared server at StoneGround. However I have found the simplest approach is to maintain separate version numbers, which are displayed on each screen and then save as a new version locally to FTP to my hosting. The users have a simple web location and qr code to install for first time and new updates. I adjust index.html to load the latest version through a meta tag. I now have no problems with updating on Android or Apple as they are treated as different software apps with their home page installations. It’s quick and simple and gives me simple version control.
I have found that updating works ok if I completely delete all my app code and data on the server prior to uploading all the files for the new version. I’m using IIS shared hosting
I’m unfamuliar with stoneground. Google doesn’t even have a reference to them. What hosting system do they use? You may want to look into another hosting system. I use aws, but i don’t suggest it for simplicity. I’ve heard good things about Hostgator.
It really sounds like TTL is the problem.
Obviously your solution works and provides you with version control, so I see no reason to change that, but the TTL is going to byte you some day.
I also update all files in the root directory of all of my app studio apps on the server, not just code.js.
My mistake. I meant SiteGround and I really appreciate your interest. 
Either way I was having updating problems using SiteGround or Volt Server with ‘code.js’ (at least in a timely manner for my testing).
Now everything is predictable and virtually instant. I just remove older versions as folders (each named by appname plus version number) at will. The users still use the one link to install and update, which I present as a url and QR code with basic installation instructions on a web page.