Thank you, I'll work on it.

Where can I have more info about depsgraph system and how noop() is calculated, since this is the function that is used to check if a node operation is useful or not and the algorithm still remove useful operations.

By the way, I saw that most of the removed operations were entry/evaluation/exit operations, so I wonder if thoses node are automatically setup as noop() ?

I committed the solution in rBe276558a50f0. In the end, it wasn't caused by the removal of no-op relations at all; this removal just made the mistake visible. It was caused by setting a property is_user_modified on a node while looping over its outgoing connections. Since rBe276558a50f0 removed those connections, the loop wouldn't do anything, and thus that property wasn't set. I moved the code to set the property outside of the loop, which resolved this issue.