I would suggest reviewing the instructions on the wiki:
http://rayshobby.net/mediawiki/index.php?title=Python_Interval_Program_for_OSPi#Updating_the_program
It might be a good idea to use a new SD card also especially if you have had logging enabled.
The files from your old installation that contain your settings are:
sd.json – contains the option settings and other preeferences
snames.txt – contains station names
programs.json – contains irrigation program configurations.
Dan