I have encountered this problem before, but I'm not sure if this is the same as what you have. I found that regardless of whether the custom URL scheme in Message.app is configured, it is determined when the message arrives, and not when the user sees the URL.
This means that if you send your own scheme URL to the user before downloading the application, this link will never be clickable even if they start downloading the application later. I tested this behavior only on iOS 7.1 (did not check other versions).
In my case, I canβt guarantee that the user has already downloaded the application when sending the message, so my solution was to use the standard URL http:// , which redirects to the user URL myapp:// on the server with redirect 302. I hope this helps!
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