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You can pass a reference class with a CLR array to a native function, and modify the class, using PInvoke services.
Example
Compile the following native library.
// modify_ref_class_in_native_function.cpp
// compile with: /LD
#include <stdio.h>
#include <windows.h>
struct S {
   wchar_t* str;
   int intarr[2];
};
extern "C"  {
   __declspec(dllexport) int bar(S* param) {
      printf_s("str: %S\n", param->str);
      fflush(stdin);
      fflush(stdout);
      printf_s("In native: intarr: %d, %d\n",
                param->intarr[0], param->intarr[1]);
      fflush(stdin);
      fflush(stdout);
      param->intarr[0]=300;param->intarr[1]=400;
      return 0;
    }
};
Compile the following assembly.
// modify_ref_class_in_native_function_2.cpp
// compile with: /clr
using namespace System;
using namespace System::Runtime::InteropServices;
[StructLayout(LayoutKind::Sequential, CharSet = CharSet::Unicode)]
ref class S  {
public:
   [MarshalAsAttribute(UnmanagedType::LPWStr)]
   String ^ str;
   [MarshalAsAttribute(UnmanagedType::ByValArray,
        ArraySubType=UnmanagedType::I4, SizeConst=2)]
   array<Int32> ^ intarr;
};
[DllImport("modify_ref_class_in_native_function.dll",
           CharSet=CharSet::Unicode)]
int bar([In][Out] S ^ param);
int main() {
   S ^ param = gcnew S;
   param->str = "Hello";
   param->intarr = gcnew array<Int32>(2);
   param->intarr[0] = 100;
   param->intarr[1] = 200;
   bar(param);   // Call to native function
   Console::WriteLine("In managed: intarr: {0}, {1}",
                       param->intarr[0], param->intarr[1]);
}
str: Hello In native: intarr: 100, 200 In managed: intarr: 300, 400