I have tried to reproduce the problem on a smaller scale in order to get you something manageable, and I can't reproduce the error in other contexts, but in my production context it happens all the time.

This is what I am doing: I am running batch transformations. 

I run a process that transform a bunch of XML documents to HTML and saves the result in another DB.

In both cases, I am processing the exact same set of documents, the exact same way. It's all going through the exact same code with the exact same parameters and called from the exact same web page. 

After the crash, the database seems corrupted, I have to delete it to avoid getting the same error all the time. If I try to add the DB as a logical folder in XML Oxygen, I get a 500 error.

The DB indicates (DB properties in BaseX GUI) that, on the second run, the process was able to save the HTML documents and crashed after (the trace that I left indicates the same thing). 

If I do not delete the collection and then run the process multiple times, I don't get a crash.
If I run the process, then comment out code so only the collection deletion occurs. The collection gets deleted and the DB is NOT corrupted. If I run the process again to repopulate the DN, it crashes

Because of the exception about ~webdav DB in the trace, I thought it was my fault for deleting the DB by error.

Now, my impression is that something happens when the collection is deleted that leaves the DB in a different state than the one it was in before the collection existed. This 'something' causes the crash to occur.

If I put a stop after the delete, I can see that the delete function itself worked and did not cause the crash. I can go in the GUI, open the DB properties window and browse up to where the deleted collection was.

then (db:delete($db-name, $dir-to-delete))

case 'create-and-save-html-files' return (staticHTML:create-and-save-html-files($param-map),
                                                     db:output(admin:display-in-dashboard($progress)))

return (for $submenu in $submenus
            let $pos := index-of($submenus, $submenu)
            let $debug := file:append('debug-crash.xml', 'In create and save, before debug sub
')
            let $debug := file:append('debug-html-submenus.xml', concat(' In pos ', $pos, '
'))
            let $debug := file:append('debug-html-submenus.xml', $submenus[$pos])
            let $debug := file:append('debug-crash.xml', 'In create and save, after debug sub
')
            return db:replace($app:review-db-name, $submenu-destinations[$pos], $submenu),
            (for $test in $index
            let $debug := file:append('debug-crash.xml', 'In create and save, before index sub
')
            let $debug := file:append('debug-html-submenus.xml', ' In index... 
')
            let $debug := file:append('debug-html-index.xml', $index)
            return (db:replace($app:review-db-name, $index-html-destination, $index), file:append('debug-crash.xml', 'In create and save, after index sub
') ))
            )

All debug traces (file:write/append) get written and all files have HTML content. So the next step would be to exit the function and go back to the calling function for the db:output... I never seem to get out if the functions are called after the deletion of a collection.