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Deleting zombie entries in left-hand pane and data loss


Hi all
I have a recurring problem: 

I like and use the hierarchical page index on the left hand side a lot and populate it using 1) adding subpages by typing 
Or 2) right-clicking on a page choosing “add subpage” 

From time to time, “zombie” pages turn up in the index, either because the page itself is only implied but has never been visited and is therefore empty or though some other happenstances.

Selecting it and choosing “delete page” from the context menu leads to all kinds of unwanted effects, most notably by making some OTHER page disappear (not the selected one) and rendering all index pages below the selected one invisible in which “below” means entries physically lower on the screen not hierarchically nested under..
Now, some of those pages reappear after closing and restarting Zim but for an app I depend upon so much this behaviour makes me very nervous. 

A related question: 
I use git as my version control system with the optional Zim plugin, which is extremely useful for tracking how the content of a page has changed over time. Can this git repository also be used to investigate how a subtree has changed? In the above example I know where in the hierarchy I deleted a page, hence where some other page might have gotten deleted accidentally but so far I have not found out how this information can be extracted from the Zim repository. 

Do others experience the same and have a solution maybe?

Many thanks 

macOS High Sierra
Zim 0.67

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