BigOven doesn't delete recipe boxes during install/uninstall without the user explicitly indicating they'd like to delete the recipe boxes.
Instead, it sounds like BigOven is simply looking in a new default location for the recipe boxes. Note that about 2 years ago, we moved the default data install location from the "My Documents" area to the "Shared Documents" area of your PC. If you've got a copy of BigOven that is several years old, that's likely the case.
The best document we have to tell BigOven where your "My BigOven Recipes" folder truly is, is here:
http://www.bigoven.com/docs/regedit.htm
Double-check that it's pointing to the correct location. We strongly recommend you move your old "My BigOven Recipes" folder with the latest recipe boxes to the "Shared Documents" folder.
Also see the post, "Where BigOven looks for files", at http://www.bigoven.com/cs/forums/t/3947.aspx