Sorry about the trouble Berto.
This is a one time only change. Yes, you will have to redo configuration, unless you use registry trick. Here is how:
Save [HKEY_CURRENT_USER\Software\JRiver\Media Center 12\TV Settings]. Open it in an text editor, and insert "\Zone 1" (or "Zone 2", etc.) behind "\TV Settings" in every instance.
For example, change [HKEY_CURRENT_USER\Software\JRiver\Media Center 12\TV Settings] to [HKEY_CURRENT_USER\Software\JRiver\Media Center 12\TV Settings\Zone 1], and change [HKEY_CURRENT_USER\Software\JRiver\Media Center 12\TV Settings\Digital Channels] to [HKEY_CURRENT_USER\Software\JRiver\Media Center 12\TV Settings\Zone 1\Digital Channels], etc.