It depends on what custom configurations you made.
If the resources involved are shared resources (files, folders, printers) and the custom configuration only involves access/share permissions, running dcpromo shouldn't affect anything as access permissions are a function of NTFS.
If you made "custom" changes based on user rights to the domain security policy (vs. the local computer security policy) then yes, these changes would be lost.
If you have services such as DNS or DHCP running, these will continue to run successfully (mostly) whether your server is a DC or not. The exception is if you are running DNS in Active Directory-integrated mode. Running dcpromo removes Active Directory, so you could lose your DNS tables. The way around this would be to change your DNS zones to standard primary zones before running dcpromo.
You can't truly "move" a DC from one domain to another. You must run dcpromo (demoting the DC), move and join the server to the new domain, and run dcpromo again (promoting the server back to DC in the new domain).
Hope this helps.