[Shkutu]

Debugger, можно, читаем справку про Check parameters

Код:

 [Files]
Source: "A\MYFILE.TXT"; DestDir: "{app}"; Check: MyDirCheck(ExpandConstant('{app}\A'))
Source: "B\MYFILE.TXT"; DestDir: "{app}"; Check: DirExists(ExpandConstant('{app}\B'))

 [Codе]
function MyDirCheck(DirName: String): Boolean;
begin
  Result := DirExists(DirName);
end;