This is not the tip of an iceberg, but of an ice-cube ;-)
You just have forgotten to disable again the "Suppress API Gen" for some pins which has been enabled in the original code.
Thank you, Bob. You're right.
I never used the function CY_SUPPRESS_API_GEN.
Apparently I copied this from another project.
It is curious how much I win if I use CY_SUPPRESS_API_GEN = true.
I never really thought about it.
Yes, by disabling code generation you have the opportunity to change some of the originally generated code without the effect of being overwritten at the time of a new build.
I consider this solution only as an intermediate state or for a QnD hack since it may not follow a component version change or a compiler upgrade. I even delete from time to time the folder "Generated Sources" in Creator to do a "Clean and build" from scratch or to get smaller archives. Since I never follow the way of including my interrupt handlers into the generated files I am fine off with that.