Most browsers currently have a limit for message size:

https://stackoverflow.com/questions/15435121/what-is-the-maximum-size-of-webrtc-data-channel-messages

My testing on chrome gets the following error:
Attempting to send message of size 988606 which is larger than limit 262144

Although the spec is expected to be built into browsers, these arbitrary size limits result in no error message that I see in the console. The above comes from running debug version of chrome.

When I tried to create my own 'sync' system before switching to try y-webrtc, I used protocol buffers to wrap updates, and hashed the data to keep them order/organized. I don't have any real knowledge about best practices, however.