Hey Jbelix,
Sorry to hear that your guild reputation has been reset.
While we don’t have any known bug for this issue at the moment, it looks like we’ve seen similar reports recently, and the developers should be looking into it soon.
As for your second issue, if you’re saying that some reputations aren’t appearing in your reputation tab anymore, this may be an addon issue. Could you try to disable them please, or reset your interface?