You can't implement __COUNTER__ directly. The preprocessor is purely functional - no state changes. A hidden counter is inherently impossible in such a system. (BOOST_PP_COUNTER does not prove what you want can be done - it relies on #include and is therefore one-per-line only - may as well use __LINE__. That said, the implementation is brilliant, you should read it anyway.)
What you can do is refactor your metaprogram so that the counter could be applied to the input data by a pure function. e.g. using good ol' Order:
#include <order/interpreter.h>
#define ORDER_PP_DEF_8map_count \
ORDER_PP_FN(8fn(8L, 8rec_mc(8L, 8nil, 0)))
#define ORDER_PP_DEF_8rec_mc \
ORDER_PP_FN(8fn(8L, 8R, 8C, \
8if(8is_nil(8L), \
8R, \
8let((8H, 8seq_head(8L)) \
(8T, 8seq_tail(8L)) \
(8D, 8plus(8C, 1)), \
8if(8is_seq(8H), \
8rec_mc(8T, 8seq_append(8R, 8seq_take(1, 8L)), 8C), \
8rec_mc(8T, 8seq_append(8R, 8seq(8C)), 8D) )))))
ORDER_PP (
8map_count(8seq( 8seq(8(A)), 8true, 8seq(8(C)), 8true, 8true )) //((A))(0)((C))(1)(2)
)
(recurses down the list, leaving sublist elements where they are and replacing non-list elements - represented by 8false - with an incrementing counter variable)
I assume you don't actually want to simply drop __COUNTER__ values at the program toplevel, so if you can place the code into which you need to weave __COUNTER__ values inside a wrapper macro that splits it into some kind of sequence or list, you can then feed the list to a pure function similar to the example.
Of course a metaprogramming library capable of expressing such code is going to be significantly less portable and maintainable than __COUNTER__ anyway. __COUNTER__ is supported by Intel, GCC, Clang and MSVC. (not everyone, e.g. pcc doesn't have it, but does anyone even use that?) Arguably if you demonstrate the feature in use in real code, it makes a stronger case to the standardisation committee that __COUNTER__ should become part of the next C standard.