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I think that it might be a matter of file permissions. If you find that a saved scenario loads, but 'create a flight' does not load any of the intended conditions, you may have a file 'locked' because it has a permissions-required level too high for your login.
Pay attention to what account you install it from. If installed with an Administrator account, you may find its files aren't allowed to be altered, because there are Administrator-owned. So you might want to simply install it from your usual Windows login, the same one you intend to use it with.
I'm honestly puzzled by such difficulties, but have recently encountered them and not yet quite found a clean, neat, instant solution. But I offer the above thoughts.
Also, after you accidentally deleted the account, the remains of the old installation may need to be cleaned out, or they may be interfering with the new installation... which is not the problem in my case, but it's a thought about your problem, to consider.
What version of MS F.S. do you have? What Windows is it installed upon? Have you run an Update on your MS F.S. ?