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My guess is that there is a race condition in the Qt Windows code. When the second instance loads the clip library it sends a signal to invalidate the contents on the first instance and force a reload. But if that signal to reload comes before the second instance has dropped its file lock on the clips file, the first instance comes back with nothing (ala a race).
This is just a guess cause the code involved in Qt is quite complex and platform specific.
If this guess is true, then opening a third instance of Sigil and then adding something to the clip library should send a signal to the first two instances to reload. This should give it a chance of making the lost clips re-appear in the first instance.
Would someone who see this problem on Windows please try adding a couple of new instances of Sigil and then if one loads properly, edit the clips library to add something from it and see if that forces the other instances of Sigil to resync.
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