Warning for iPhone 7 users: You could lose your favourite apps in setting up your new phone

Plugging in an iPhone 7? When you sync to the cloud outdated apps might not make the cut.

People installing their new iPhones 7 today could find their favourite old apps, and any data they contain, will disappear without warning as part of Apple's program to clean up the App Store.

Apple this month embarked on a program to evaluate the more than 2 million apps in the App Store and kicking out apps that have been abandoned by app developers and not updated so that they are no longer compatible with recent operating system upgrades, crash as soon as they are opened or present other risks to iPhone users.

It is not clear how many apps will be removed from the App Store in the clean -up but it will likely to be in the tens of thousands or possibly hundreds of thousands. Those figures are educated guesses because Apple has not put a number on it.

According to analyst firm, Adjust, a quarter of apps in the app store have not been updated since November 2013. Another app analyst group Sensor Tower says more than 300,000 apps have not been updated in three years.

Removing the apps from the App Store does not remove them from your device. If you install iOS 10 operating system that was released this week, the apps will remain on your device.

But when you set up a new iPhone by installing a backup from the cloud, those apps which are no longer in the App Store will not install as part of the back up.

Certainly, most of the apps that will disappear from the App Store won't be missed. If that "make a fart sound" app you deleted years ago disappears from your iPhone, you probably won't notice.

But this issue came to our attention in the past week in the most obvious way: the two apps I use everyday have been kicked off the App Store and apparently have gone for good.

As a keen runner, I have logged every run I've done in the past eight years in an app called Pace, so that I have a record of pace, distance, time and the number of kilometres I've run in every pair of shoes.

The app was very limited in functionality but was still perfectly functional for me. Because it was so old and so limited, the data was not kept in a cloud service. You could export the data from it, which I did recently as a backup, but the export was corrupted.

The app has gone and my data has apparently gone with it. I have approached Apple to see what people can do in this situation but so far there is no solution that works for me.

It is understandable why Apple removed Pace from its App Store. The app had not been updated in about five years. The website offering support for the app no longer exist. And when I tracked down the maker of the app through social media, he did not respond to questions about what the users of his app should do with their years of data to keep the record going.

The other app that disappeared from the App Store that I used daily was FlickStackr, a once very popular app created by a Canadian photographer and app developer Carlos Mejia and his wife.

Mejia detailed how his app was removed from the App Store.

"I got an email from Apple stating in a very legal non-personal way that our developer account had been terminated because we had broken the agreements," he says.

"Which part? Why? It didn't say. I called in to support. The response `it's all in the email'. No details. And we're in the doghouse for one year. Apps are gone. Sales reports. Stats. All gone. No appeals."

"I thought to launch it again, but then some of the favourite features will be gone, and the truth is that I don't have time. And we will only sell a few per month. Not worth it anymore."

What can you do about it if you think your favourite app is about to get the boot?

Before you get rid of your old iPhone, consider which apps you use frequently and, particularly, those that contain data you don't want to lose. Check to see if they are still in the App Store.

If they are not in the App Store, back-up any data they contain in any way you can, and see if you can find an alternative app that will suit your needs.

Apple cleaning up its app store is a good thing, because it means that there will be fewer apps that crash as soon as you open them or have other failings because the app developer has left them to die.

But even good things can have unfortunate consequences.