You have to be careful when you write to the radio or read the radio if you have anything programmed different than the database.
I strongly recommend copying the SD card's BCDx36HP directory when you have the radio mounted (USB Mass Storage mode) before you do anything. That way, if you do f'up, you can restore.
For instance:
I have extensive bounding boxes (GPS rectangles) programmed into every FL's system and department I have in 2 states.
If I do any appends to favorites from Sentinel, then write to the radio, I have to be careful I don't overwrite all of my custom work.
Same goes for reading the radio. If Sentinel has all of your changes, reading the radio will overwrite them.
Tip:
ProScan is really good for editing favorite lists.
Search/replace and location control mapping are awesome.