As for savegames, there have been many, many patches with new content. Other content got removed. If you played Discovery in Singleplayer, that is probably all outdated. If you played Discovery or other mods or just plain vanilla, the savegames get deleted automatically whenever you play a different Freelancer version.
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You can preserve your saves by going to My Documents/My Games / and renaming the freelancer folder to something like 'Freelancer backup' - to preserve your vanilla savegames
And if you want to play vanilla, rename the Freelancer folder to 'Freelancer Discoverybackup' - then rename the freelancer backup to just Freelancer