If you simply overwrite an existing version of phpnuke with a newer version I wouldn't expect it to work at all, overwriting is not upgrading. I don't know what version of phpnuke you were upgrading from but you may run into all sorts of issues that may even include the db.

Did you follow the upgrade instructions included with 8.1?

Whenever possible, it's always best to copy your existing site and do a test upgrade on a separate account. I know it may take longer and can be a pain in the @rse but its a safe way to not screw up your existing install.

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