Here is what Proficy Machine edition has to say about that warning:
Warning 12539: Memory area has unassociated value(s) [%[memory area]]
During an upload from a PACSystems, a non-zero initial value was found in the memory area mentioned in the Feedback Zone, but no variable is mapped to that memory location. No variable is being created in Logic Developer - PLC to contain that value. If you are using initial value data tables, that non-zero initial value is not uploaded to a table.
Example
A memory range has been defined for a module status, but no variable has been defined to refer to that memory range.