I am using Hibernate 5.2.11 with Bytecode Enhancement.
All my entites are with @Proxy(lazy = false) and all my to-one relationships with @LazyToOne(LazyToOneOption.NO_PROXY).
In addition to that, to preserve the business logic of the system (we are migrating from Kodo to Hibernate) I needed to add to every @ManyToOne annotation CascadeType.PERSIST option.
It sometimes causes execution of the which ends up in the first condition
For some days I have been trying to provide a test case that reproduces the issue but I found it very hard to create, because when I am debugging the execution flow of cascading persist operation I have different result than when running the program in a normal way. When debugging line after line I reach the condition above and a field value becomes null (so the insert value does) but when running the test in a normal way, everything is okay.
Do you have any idea how to deal with it and why is this happening that I got different results with debug and without it?

The debug has an Inspector section which triggers the Proxy initialization. The only way to test this kind of issues is with Unit Tests, not via debugging.