No, your conf files will not be affected.
Assuming you use UnrealIRCd on Linux or another variation of Unix, use the following:
cd Unreal3.2 (may be Unreal3.2.7)
make clean
./Config
When it asks about prefixes ~ and &, say Yes, that you want them to be included and used.
When Config has finished, run make.
If, however, you are using UnrealIRCd on Windows, you will need to visit the UnrealIRCd and download the Win32 version that includes the prefixes and install.
As said, .conf files should remain untouched by both the compiler and the installer, though it is a good idea to keep up to date backup copies before making changes like this, unless you know exactly what you are doing.