So - couple things.
COBRAS includes a tool called "backup editor" that's designed to help change the alias and/or extension numbers for users in the backup database itself to help when migrating between systes that have some changed alias naming conventions (this is a common scenario I call "while we're migrating, lets fix everything all at once").
The typical process here is:
1. get a backup of the old system
2. Install your Connection server and import your users (in this case you're LDAP users from AD).
3. edit a copy of your backup database (please make a backup copy first) so the aliases match the users from AD
4. Import your users from COBRAS over existing users in your Connection.
Doing it this way ensures you got all the aliases and extensions correct - in other words on the COBRAS user conflict page ALL users should be set to overwrite existing users in Connection - if any of them show "Create new" you know you screwed something up and you can adjust and try again.