I've got a possible solution. Grab one of the SQLite .NET packages and just have the archiver update the nxTools dupeDB directly. Just make sure you don't use one huge transaction during the move as that would lock the DB while it's copying files.
Update: That might be complicated by the fact that nxTools uses a really old modified SQLite which ignores case. You can get that same behavior in current SQLite releases without any modifications by asking for it so we might need an "updated" version of nxTools. I can and should probably do this for everyone anyway...
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