I am not sure how that can even happen as program tries to save it multiple times even if something else is preventing writing to disk.
It could happen if portable path is in a cloud synchronized folder (then there is no way of knowing what cloud sync software is backing up or restoring),
or if the entire program folder was moved while OC was still running (then it is saved in old program location)
Open \Settings\Favorites.json to look for old paths (unless you closed it already and it saved the default paths only)
You can also look for log file in \Logs folder on the date of the previous run or at time when you noticed favorites missing
There would be an error following by "Could not save collection of paths to file"