It shouldn't, and anyhow, the directory synchronization by default take place every 6 hours, and if then CCM will delete those accounts from its own directory table after 24 hours that it was marked as inactive.
Please notice that CCM is not going to make any changes to the accounts; it will just sync them with it's local directory table.
You can add another directory entry in CCM before you proceed with the deletion of that one, just make sure that a Full Sync is performed after you have the directory the way you want it to be.
Check this link for more information about the LDAP integration in CCM 5.X:
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