Saves the new version of the file with right numeric postfix. For instance, ex.ma will be saved as ex_01.ma. ex_02.ma will be saved as ex_03.ma, etc.

SaveMayaSceneWithRightNumber.py

import maya.cmds as cmds
import re
import maya.mel as mel

def MSpress():
	global initTS
	initTS = cmds.timerX()
	
def MSrelease():
	global initTS
	hTime = cmds.timerX(st=initTS)
	if hTime > 0.4:
		scenenm = cmds.file( q=1, sn=1 )
		spltname = scenenm.rsplit("/", 1)
		m = re.search(r'\d+$', spltname[1][:-3] )

		# if the string ends in digits m will be a Match object, or None otherwise.
		xName = 1
		clName = ''
		nName = ''
		if m is not None:
			xName = xName + int ( m.group() )
			clName = re.sub(m.group()+'$', '', spltname[1][:-3])
			nName = clName + "%02d" % ( xName ) + spltname[1][-3:]
		else:
			nName = spltname[1][:-3] + '_' + "%02d" % ( xName ) + spltname[1][-3:] 
		cmds.file( rename=spltname[0] + '/' + nName )
		cmds.file( f=1, s=1 )
	else:
		mel.eval('checkForUnknownNodes(); FileMenu_SaveItem')