No problem, we can investigate this further. Please try updating to VisualGDB 5.6 Beta 5. If the problem persists, please try reproducing it on a clean project from scratch and sharing the repro steps we could follow on our side per our problem reporting guidelines.
We have just rechecked the sha1-internal.c file on ESP-IDF 4.3.1 and it worked just fine (it was not used by default until we manually disabled mbedtls crypto), so the issue could be specific to a particular project or a particular machine.
Either way, adding the __SYSPROGS_CODESENSE__ wrapper will not affect the build results (this macro is only set by the IntelliSense engine), so it should be safe to do even for library files. Due to the optimization used by VisualGDB to handle large file sets, hiding specific files from IntelliSense would be rather non-trivial, so unless the __SYSPROGS_CODESENSE__ workaround breaks specific functionality, we would advise using it instead.