You can try to export and import the bootloader component to be customized component, then your own code won't be modified by build and compile.
Thank you, Ryan. Sounds like this is what I want to do. Will give this a shot!
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Another option is to make use of the pre-build option in the IDE, and create a simple batch file or Python script or whatever you prefer which copies the modified source file(s) from some special location that you have prepared into the appropriate /Generated_Source/... subfolder for your compile architecture.
There are pros and cons to each approach, but if the component customization approach is harder or more complicated than you anticipated, you might try this instead.