Alex and Berto,
I hope the following will answer your questions, at least partially:
1. Frequency override is saved in a registry key under Microsoft. Here is the location:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\TV System Services\TVAutoTune\TS#-?
where # is your "Country Code" (1 for USA, 31 for the Netherlands etc.) and ? is 0 for antenna, 1 for cable. Notice that this is under HKEY_LOCAL_MACHINE whereas the regular TV channel information for MC is saved under HKEY_CURRENT_USER.
Media Center does not mess with that key unless you actually carry out the "Frequency override" procedure. So I do not know why you would lose that information. You may want to backup that registry key for the future.
2. The correct location for TV channels, as you already know, is
HKEY_CURRENT_USER\Software\JRiver\Media Center 11\TV Settings\TV Channels
If you also have a digital TV card, the digital TV channels are in a separate location, at
HKEY_CURRENT_USER\Software\JRiver\Media Center 11\TV Settings\Digital Channels.
The other location you referred to,
HKEY_CURRENT_USER\Software\JRiver\Media Center 11\Properties\TV Channels
is an artifact of older version, as well as some weird implementation details. Even though the information under that key actually duplicates the information under the two keys (for analog and digital) above, it is volatile. Thus you (as a user) should just ignore that key.