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How exactly are you uninstalling 8.0? I have been migrating users to 8.7 for a few months now and we also use Notes and I have not seen this error. One thing you might want to consider is going into the On Delivery Email Scan Policy for 8.0 and disable that in the Scan Items tab. This should stop the NCDaemon.exe that is running so it won't tie your VS client to the Notes client. Again, knowing how you are removing 8.0 would be helpful.
I'm using ePO 3.6.1 and running the uninstall of 8.0 as a deployment task. I will give disabling the email scan policy a go though, thanks.
We're currently in-between a Domino upgrade as well, from 7 to 8.5. Clients running the 7.01 client get the error, however clients running the newer 8.5 client don't.
If your VSE 8.0i clients are not on Patch 16 prior to upgrading to 8.7i (actually, it's if you try to remove 8.0i) then you will encounter Notes issues.
Refer to the Patch 16 readme for resolved issues applicable to Lotus Notes.
Patch 16 did the trick, thanks for that one.