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Sounds like the DB is corrupt. This may require some help from support. However, a quick fix is to create a new Data Folder. When you are running through System Settings for Server, point to that new data folder. This should resolve the collections error you are having. The only catch is that you will have to re-upload your collections. See screen shots below:
@RsRoel Did you ever find a solution for this? We ran into the same issue and haven't got any luck solving it. We don't want to lose all the settings as you mentioned you did. Please let me know how did it go.