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I do this slightly differently (in Project Probe). Yours might be faster if you only look at link info from the file rather than loading the hierarchy but I have to look at lots of other VI stuff that require opening the VI anyway too (like re-entrancy, debugging enabled, icon, description etc). I also use it to sort VI refnums when force compiling hierarchies. I create the file list similarly to you then I open each VI and check if it has dependencies (Get VI Dependencies Method Node). The VI opened and its dependencies are added to a [found] list. If a VI in the file list is already in the list or in memory then it doesn't need to be opened and could be considered already processed (it has a parent that was previously opened). If a VI has no parent and has no dependencies then it is an orphan. It can also find VIs in conditional disables. So I deduce if it is an orphan from the dependencies of all the VIs

Use a prepared statement and a transaction. Your current implementation requires writing for each iteration which is slow obviously. Check out the "Insert many rows code template" on the SQLite Library >> Code Templates palette. The prepared statement will allow you to use binding which is very useful as it maintains data types in your application. See following Picture for an example (I can't test it right now, but it should work like that):