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Discovery settings changing after running config wizard?

Has anyone else run into this? The configuration wizard ran during an upgrade to NTA 4.2, which seems to have knocked out some of the settings I had in my discoveries. I love the "Define Monitoring Settings" feature in the Sonar Wizard, it's what keeps my nightly discovery from gobbling up all those useless WAN Miniport interfaces

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For some reason, after the config wizard ran, the filters in the picture above were wiped out and all of the checkboxes for status, port mode, and hardware were selected. Additionally the IIS, SQL, and Exchange monitors under the Applications section were changed to be included in the discovery. Needless to say the next morning our polling engines were overrun, and it took a few hours to manually delete the thousands of newly imported WAN Miniport interfaces and the hundreds of AppInsight monitors. Maybe this was a fluke, but it seems like this shouldn't happen?