Corruption can happen anywhere in a database including the security section. It generally makes everything unstable and my recommendation is to export all of your data and go back to a previous clone. It is good to hear that you can log in at least to export the data. Do not count on ever using this database in the future because issues like this may seem fixed, but then funny things happen down the road.
By the way, I've seen this happen a lot, but never on a server hosted database. For this reason, I always recommend my users with important data always use the FileMaker Server. The FileMaker service is a true system service and not an application. All applicaitons are subject to user interface issues and crashes. But if you're hosting the database via an application, if you crash, it often corrupts the databsae. While it can often be recovered, repeated recoveries eventually will catch up with you and make strange problems in the database or sometimes even useless. Be aware that recovery helps, but it is not a guarantee that everything is fixed and working.