I am not sure if I can be of much help, but let me try one suggestion. Instead of a "Cut and Paste", do a "Copy and Paste". This will take longer to do and requires twice as much disk space, both of which are undesirable things, but it seems (and I am in no way sure about this) Winders (in an apparent attempt at being helpful) sometimes remembers when you "Move" a file and later when you attempt to access the file where it "was", it will redirect the access to the new place where you moved it "to". Thus when VDV was building the list of clips, it may show the file no longer exists because it did not "know" that you moved it, but when you direct VDV to delete the clip, it may be using a function of Windows that knows of the "move" and thus goes and finds the moved file and deletes it. (Now, ain't that helpful?

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If you do a "Copy and Paste" then VDV will find the original clip and you can then tell it to delete it (if you need the disk space) and Windows will just delete that file and not the copy.
I suppose you could also do a "Copy and Paste" and then Delete it all using Windows and then clean up the VDV databases, but I'd recommend not deleting the files outside of VDV. VDV does seem to cleanly handle the "user deleted files scenario" without later repurcussions, but why take the chance of confusing it?
Another thing to try is to use VDV to "export" the files to some other place. Right click on the desired clip, either in the list on the left side of the View mode or the large display in the View mode and select "Export Clip" from the Context menu.
It is a little more work, but you can even export clips where there has been no motion at all. if you have more than one camera you must select just a single camera from the "Camera" drop down list and then select a clip where motion was detected (by rule or not) adjacent to the time you want and then drag the time thumb button to one end and then click the FWD or REV buttons (the ones directly adjacent to the RUN button in the middle, not the arrows in the circles at the extreme ends) to move the time to the next clip, and you will get the clip that is next in the time sequence, whether there was motion or not. If it is a non-motion clip the highlight in the left hand list will be between the clips saved because of motion. You can then right click on the large display section to get the Context menu and select "Export Clip".
To convert the files to WMV I use Windows Live Movie Maker without having a problem with playback speed. What programs have you tried to convert MP4 to AVI? Maybe they could handle WMV to AVI better... although first using Media Player would entail that additional intermediate step, at least with Movie Maker you have the option of trimming the output to just the relevant portion.
Hopefully, the folk at VDV that really know this stuff, will come along soon and provide better info.