If you are halting your code to allow user intervention you will need to alter your code to take this into account.

You can use a public variable to store the state of the macro execution.

This is only pseudo code.
Public g_blnMacroRunning as boolean

Sub MyCode()

   if not g_blnMacroRunning then

      ' do first part of macro
      
      g_blnMacroRunning = True

      ' Left user do his thing
      Exit sub
   endif

   g_blnMacroRunning = False

   ' do second part of macro

End sub
If you need more help you will need to, as Dave points out, provide more information.