Check in the back of your machine for the Management Data card. It should have the encoder offsets recorded on it as well as the stroke end limits. Once those are set, you need to re enter your fixture offsets as well as your tool offsets etc.
Reloading software flushes all memory, so that is why it's highly recommended to back up first.
Newer controls do this automatically, older controls require a utility disk. Most all machines can at least use the data pip function to make a text file of the parameters , but saving the PBU files with the utility is the best way.