One way to handle this could be to use the command line tools instead. And add one book at a time in a script.
That way you can easily keep track of what books have been added and resume from the point where it failed. Most likely it would be a little slower, and require some scripting, but it would probably be much more reliable. And the script could run in the background in a terminal window while you sleep or do something else on the computer. (Not using Calibre.)
http://manual.calibre-ebook.com/cli/calibredb.html
If you have those 44K books in some sort of hierarchical folder structure, you could even add the path to the metadata when you add the book. That would most likely make it easier to add tags and other fields to make that library more manageable.
And good luck finding anything better than calibre...
