I suggest a fresh install of the game.
BUT:
if you want to play with some online Chacarcter again then you need to do this:
What is my multiplayer account id? (MP Acct id)
Your multiplayer account id is a specific identifier that is created when you first connect to the internet. This account id will remain until you a full uninstall of the game. The ID is used to identify which characters on a server are yours, allowing only yourself to play them. Uninstalling the game and reinstalling will generate a new MP Account ID. If you wish to retain your account id, before uninstalling navigate to your Freelancer folder, and then into the Exe folder. You will find a file called “myflaccountid”, which if you double click will display your number. I suggest you save the file elsewhere on your computer, or write the number down.
How do I get my old accounts back after re-installing
Firstly you should have saved a copy of your account ID as above, and then written it down. When you reinstall, if you then connect to the internet, your account ID is generate. You may overtype the new ID with your existing one, and then proceed.
That is taken from the Freelancer Multiplayer Forum, first sticky (FAQs)