Usually the code between the Start and the End are kept unchanged.
I prefer not to mess in generated code. When using the isr_StartEx() API you may declare your own interrupt handler in your code.
Could you please confirm whether you are placing the customized code between the default locations of /* `#START */ and /* `#END` */? By default, PSoC Creator would retain custom includes, defines and code between them.
Please make use of this Knowledge Base Article to retain modifications in Generated Source Files after build Avoiding changes in the source file to get overwritten in PSoC Creator