I am currently contacting Microsoft Support on the same issue. My initial access is that Windows Server 2012 R2 has an error processing TLS 1.2, which is the HTTPS protocol that AppleBot uses to scan pages.
Your apple-app-site association looks great.
Edit
I found that even if the validation tool doesnβt work when you visit the Safari site on the iPad / iPhone, the Open application in the xxx application exits
Update 2015-12-22
Microsoft is back to me. The problem is that AppleBot sends the next Hello client to start an SSL connection
Signature Hash Algorithms (4 algorithms) Signature Hash Algorithm: 0x0401 Signature Hash Algorithm Hash: SHA256 (4) Signature Hash Algorithm Signature: RSA (1) Signature Hash Algorithm: 0x0403 Signature Hash Algorithm Hash: SHA256 (4) Signature Hash Algorithm Signature: ECDSA (3) Signature Hash Algorithm: 0x0201 Signature Hash Algorithm Hash: SHA1 (2) Signature Hash Algorithm Signature: RSA (1) Signature Hash Algorithm: 0x0203 Signature Hash Algorithm Hash: SHA1 (2) Signature Hash Algorithm Signature: ECDSA (3)
When you look at the certificate hierarchy of your SSL certificate, you see
COMODO RSA Organization Validation Secure Server CA Certificate signature algorithm PKCS
When Windows Server receives the AppleBot Hello client application, it sees that AppleBot supports SHA1 and SHA256, but your certificate requires SHA384 support. Thus, according to http://tools.ietf.org/html/rfc5246#section-7.4.1.4.1 , the request cannot be completed and Windows Server resets the connection. Then AppleBot reports that the file was not found.
In particular, RFC5246 says
If the client provided a "signature_algorithms" extension, then all certificates provided by the server MUST be signed by a hash/signature algorithm pair that appears in that extension.
Microsoft Recommended Tool
When you need to use a validator, create a self-signed certificate. By default, Windows uses SHA1 as the certificate signing algorithm. Bind the self-signed certificate to your HTTPS endpoint, and then use the validator to make sure your apple-app-site association file is approved. You can then revert to the actual SSL certificate that you purchased.
My warning
Do not put a self-signed certificate on your production server. Create another server for testing!