If you want remove the "Please wait while I transfer your call" system prompt and replace with silence so nothing is played, go to the Management Console -> Settings -> System Prompts. Here then:
1) Press "Manage Promptsets".
2) In the new window that appears press "Copy Promptset" and give the new Promptset a new distinguishable name, e.g. "Custom Promptset", then press OK.
3) Make sure the new Promptset is selected in the "Active Promptset" drop-down menu and press "Set As Current Promptset", then press OK.
4) Search for the Prompt ID "PLSHOLD", select it and press the "Browse..." button.
5) Navigate to C:\ProgramData\3CX\Instance1\Data\Ivr\Prompts and open file "Empty.wav".
With the same method you can change pretty much any system prompt with your own.
Given that this is already possible, the topic is being moved back to "3CX Phone System - General".