if the 3cx hosted or local.
Local - Not if the Debian server has the same Ip address, and if you are using spilt dns you have updated the internal fqdn
Hosted - using sbc - just make sure sbc is up and running. Stun config should be ok, as you use fqdn to connect back to the server
Just remember , you need to switch off the old windows server before you install Debian 3cx