To execute the batch file, use Exec support function.
There should be no quotes in the Filename parameter of the Exec().
procedure DeinitializeSetup();
var
  InstallationFolder: string;
  ResultCode: Integer;
begin
  InstallationFolder := ExpandConstant('{app}');
  if Exec(InstallationFolder + '\mysql\db\test.bat',
          '"' + InstallationFolder + '"',
          '', SW_SHOW, ewWaitUntilTerminated, ResultCode) then
  begin
    Log('Succeeded running batch file');
  end
    else
  begin
    Log('Failed running batch file');
  end;
end;
If I install a test.bat with this contents:
@echo off
echo This is test
echo The provided installation path is %1
echo Without quotes: %~1
echo The current working directory is:
cd
pause
using:
[Files]
Source: "test.bat"; DestDir: "{app}\mysql\db"
I get this at the end of the installation:
