Why are versions deleted after publishing or updating a trigger?

This issue might be caused due to a low value at the max_input_vars parameter.

To fix this problem, go to PHP settings (either php.ini directly or some GUI) and change the max_input_vars parameter(3000-3500 is probably a good range to start with). Learn how to do it.

*What is PHP max input vars?
The PHP Max Input Vars is the maximum number of variables your server can use for a single function.