I have v1 and v2 versions of my software. v1 uses the registry to save settings, with lots of calls to GetProfileInt, etc. v2 now uses an sqlite db to save settings.
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If you have an #include file that is common, you could add something like this to it (with the W or A as appropriate). It would result in, at least, a linker error (compiler warning/error would depend on the flags):
#define GetProfileIntA InvalidFunctionDoNotCallMe
Windows already defines the functions such as GetProfileInt as macros to the A or W versions.