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Every time SwiftKey gets updated it is removed from the list of input methods. I don't remember having this problem before Android 4.4, but in the last few days SwiftKey had some updates and it just gets annoying. I have to set it up again in the settings as a viable input method, getting informed about the security implications etc.
Is there a way to disable this behavior, so I don't have to set up the keyboard after every update?
Seems to be a Google issue. There is a blog post on SwiftKey's support site.
Essentially:
The issue is that Google Play installs paid apps in a particular location on your phone and that in some versions of Android (particularly 4.1 on Samsung devices) this location is not available at the point in the boot process where keyboards are being switched on. So your phone does not know that you have SwiftKey, and it defaults back to the phone’s keyboard.
Swiftkey recommends: Place the SwiftKey icon on your home screen, then resetting it as your input method will literally only take two clicks. This is a known issue in Android code, and as per https://code.google.com/p/android/issues/detail?id=34880 will be fixed in the next version of Android you receive. (paraphrased for clarity)
The issue has been reported to SwiftKey who have responded with the following:
We’ve worked with Google to determine the cause of the issue. After researching this in depth, Google has told us this is a regression in the Android framework. They’ve also assured us that this will be resolved in a future update to the Android operating system
