Question: In some cryptographic protocols I have seen messages protected for confidentiality, authenticity, replaying attacks, reordering attacks, etc. 

What protects a protocol from an attacker in a privileged network position (e.g. in control of a majority of the fibre networks connecting countries) from just dropping messages altogether, thus stopping the two parties from communicating (a *“Denial Of Service”*)?

For example: if a protocol includes a sequence number, the receiver sees messages `#233`, `#234`, and `#236`. What should the receiver do if they missed receiving the `#235` message?

Answer: 
Message sequencing AND hash-tabling for a trail of backward messages. The loss of a single message is not a disaster, actually. To be not over-paranoid, implement "resend request" in your protocol. If it works and hashes are matched - it can be just a communication error. But if it fails - a line should be dropped immediately. Try to use Tor by the way, and when requesting a re-send use a different chain. That will help you greatly with low implementation costs
Not much in the cryptographic protocols themselves. But you can do other things to get around such attacks:

* Request signed read receipts, or received receipts. So, if I send a message from my phone to yours, it sends back a reply that your phone has received the message (or that you have opened it). If such a receipt is signed, your attacker might be able to drop the messages, but won't be able to hide that fact from you.
* Have another mode of communication to verify. I'll send you a message over wifi, and if I can't verify whether or not you received it over wifi, I will send you a text message over my cellular network. I might even call you. Hopefully, your attacker doesn't have serious control over both networks.
* Distribute the work of sending the message broadly. Send each message through multiple channels through a protocol that can handle such sending without displaying the same message multiple times. Perhaps this protocol is advanced enough to make sure that no one party sees all of its traffic... otherwise, you're living in a post-apocalyptic world much like the one we happen to be in. Whoops.

At the end of the day, this would probably only be an issue if you're a competitor of Verizon's or a merged TWC/Comcast, or something like that. Maybe Microsoft could build some such bullshit into Windows. But none of those corporations *would*, because they'd be hit with gigantic criminal sanctions and civil lawsuits and face legitimate market harms as well.

But... I don't think cryptography is meant to handle this problem.