Powershell is the tool
1. download the Quest Powershell commands @ http://www.quest.com/powershell/activeroles-server.aspx
2. open them (make sure to execute them as a domain admin or else you can list things but not write things to AD)
3. If you execute the following command you will get a list of all users and you can see if this checkbox is set (verify it for some user), True = set.

Get-QADUser -SizeLimit 0 | Select-Object Name,@{n=’IncludeInheritablePermissions’;e={!$_.DirectoryEntry.PSBase.ObjectSecurity.AreAccessRulesProtected}}

4. You can now set if for every user with the command:

Get-QADUser -SizeLimit 0 | Set-QADObjectSecurity -UnLockInheritance

You can test it by supplying one user, and see if it works: Get-QADUser username -SizeLimit 0 | Set-QADObjectSecurity -LockInheritance

Use it @ your own risk. I advise you to test it first in a test domain or test environment.
More on the set-qadobjectsecurity command: http://wiki.powergui.org/index.php/Set-QADObjectSecurity

In general I have around 500 users and doing this manually for each users is not possible, is there any way to get this done for all the users with different organizational unit.

I know it too late posting here, but hoping that you may got the solution and reading the comments.

Thanks,